Thanks for this, I feel like I've seen this too.

I'm 30 now, and I feel like several of my altruistic-minded friends in my age group in big companies are reluctant to work in nonprofits for stated reasons that feel off to me. 

My impression is that the EA space is quite small now, but has the potential to get quite a big bigger later on. People who are particularly promising and humble enough to work in such a setting (this is a big restriction) sometimes rise up quickly.

I think a lot of people look at initial EA positions and see them as pretty low status compared to industry jobs. I have a few responses here:
1) They can be great starting positions for people who want to do ambitious EA work. It's really hard to deeply understand how EA organizations work without working in one, even in (many, but not all) junior positions.
2) One incredibly valuable attribute of many effective people is a willingness to "do whatever it takes" (not meaning ethically or legally). This sometimes means actual sacrifice, it sometimes means working positions that would broadly be considered low status. Honestly I regard this attribute as equally important to many aspects of skills and intelligence. Some respected managers and executives are known for cleaning the floors or providing personal help to employees or colleagues, often because those things were highly effective at that moment, even if they might be low status. (Honestly, much of setting up or managing an organization is often highly glorified grunt work).

Personally, I try to give extra appreciation to people in normally low-status positions, I think these are very commonly overlooked.

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Separately, I'm really not sure how much to trust the reasons people give for their decisions. I'm sure many people who use the "overqualified" argument would be happy to be setting up early infrastructure with very few users for an Elon Musk venture, or building internal tooling for few users at many well run, high paying, and prestigious companies.

Another point I've heard made a few times (and at-least-a-little agree with):

Let's say Bob transitions from COO at a mid-sized org to finance manager at a small org. Bob has done finances before, and within a few months has set up some excellent systems. He now only needs to spend 10 hours a week on finances, and tells his manager (Alice) that he's interested in taking on other projects.

Alice doesn't currently have projects for Bob, but Alice and Bob saw this coming and set clear expectations that Bob would sometimes run out of things to do. Bob was fine with this, he's happy to spend his extra time at home with the kids.

But also... Bob notices that their HR systems could use an upgrade. He writes up a plan and shares it at the next team meeting. Some people think this is a good idea, but the HR manager doesn't want to implement the plan and Alice doesn't want to put Bob in charge of HR systems.

Bob is a little confused but shrugs and goes back to building a chicken coop.

This happens a few more times, and it's taking up more and more of Alice's time to review Bob's proposals. She likes Bob's ideas and wants to find ways to implement them, but doesn't like Bob's leadership style so doesn't want to put him in a leadership position. A couple other people in the org do like Bob's style, and are confused about why he isn't put in charge of more projects.

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So the takeaway is something like: even if you are hiring an experienced person to a junior role, you are essentially hiring them to a senior role because they think like a senior hire. If their work and ideas are not given the space to thrive (which means basically treating them as senior staff), then it'll likely be a source of tension. 

It's harder to carve out a senior-shaped-hole at an organization and higher stakes to hire someone with more seniority (which in my mind means autonomy over a budget and maybe a report or two). Organizations do this successfully all the time but it's a much more significant effort than hiring a junior role. 

Or put another way: the more agent-y the person you hire, the more you'll need to be careful about principal-agent problems. 

There is a bunch of nuance in here and various solutions, but I think it contributes to some hesitance around senior>junior transitions. 

Similar to Ozzie, I would guess the 'over-qualified' hesitation often has less to do with, "I fear I would be under-utilised and become disinterested if I took a more junior role, and thus do less than the most good I could", but a more straightforward, "Roles which are junior, have unclear progression and don't look amazing on my CV if I move on aren't as good for my career as other opportunities available to me." 

This opportunity cost (as the OP notes) is not always huge, and it can be outweighed by other considerations. But my guess is it is often a substantial disincentive:

• In terms of traditional/typical kudos/cred/whatever, getting in early on something which is going up like a rocket offers a great return on invested reputational or human capital. It is a riskier return, though: by analogy I'd guess being "employee #10" for some start-ups is much better than working at google, but I'd guess for the median start-up it is worse.
• Many EA orgs have been around for a few years now, and their track-record so far might incline one against rocketing success by conventional and legible metrics. (Not least, many of them are targeting a very different sort of success than a tech enterprise, consulting firm, hedge fund, etc. etc.)
• Junior positions at conventionally shiny high-status things have good career capital. I'd guess my stint as a junior doctor 'looks good' on my CV even when applying to roles with ~nothing to do with clinical practice. Ditto stuff like ex-googler, ex-management consultant, ?ex-military officer, etc. "Ex-junior-staffer-at-smallish-nonprofit" usually won't carry the same cachet. 
• As careers have a lot of cumulative/progressive characteristics, 'sideways' moves earlier on may have disproportionate impact on ones trajectory. E.g. 'longtermist careerists' might want very outsized compensation for such a  'tour' to make up for compounded loss of earnings (in expectation) for pausing their climb up various ladders.

None of this means 'EA jobs' are only for suckers. There are a lot of upsides even from a 'pure careerism' perspective (especially for particular career plans), and obvious pluses for folks who value the mission/impact too. But insofar as folks aren't perfectly noble, and care somewhat about the former as well as the latter (ditto other things like lifestyle, pay, etc. etc.) these disincentives are likely to be stronger pushes for more 'overqualified' folks. 

And insofar as EA orgs would like to recruit more 'overqualified' folks for their positions (despite, as I understand it, their job openings being broadly oversubscribed with willing and able - but perhaps not 'overqualified' - applicants), I'd guess it's fairly heavy-going as these disincentives are hard to 'fix'.

One reason I don't see here: if you take a big decrease in level of responsibility, it can be hard to reverse.

For example, imagine you manage a team of 10 people and a budget of $10 million at a private corporation. You're on track to eventually take on a C-suite position, which will either allow you to earn to give significantly or bring really great skills to an EA charity at that point.

If you leave the team you're managing and take two years to write Forum posts on behalf of an EA charity, you may lose the opportunity to become a CEO. Maybe that's fine - maybe you know ever cared about that because of the social status you could get from it - but maybe EA needs people with experience as successful CEOs and bringing in private sector rising stars for entry level positions is a bad idea.

I really liked CEA's "tour of duty" framing for the recent hiring rounds!  I thought that was a great signal to potential candidates of what they could expect in the job. I think employers should be more explicit with candidates about what they're expecting from new hires in terms of tenure.

Conversely, I would encourage job applicants to be candid with employers about their tenure expectations for a role. For some roles, only staying in the role for 1-2 years is perfectly fine. For other roles, especially ones that require a lot of role-specific knowledge and training, that would be harmful to the organization. I also would ask candidates to introspect honestly - do they feel that a certain role is in any way "beneath them?" It's can be damaging to morale to have a colleague who feels like the job is just a stepping stone to something else.