Venture capital economics is premised on founders accepting low initial salaries based on the hope for long-term big payoffs. Which makes it OK for seed funding to be very small (on the order of tens of thousands).
However, non-profits have no hope for long-term big pay offs and therefore have no financial incentive to seek small amounts of seed funding.
In other words, it is sensible for a for-profit startup founder to accept zero salary (or close to it). However, it is nonsensical for a non-profit startup founder to accept close-to-zero salary.
I believe the YC non-profit initiative could still be beneficial to non-profits for the sake of mentorship, networking, etc. But I don't think many non-profit founders will drop their day-job salaries to launch YC non-profit startups.
Edit: s/sensical/sensible/g