I don't presume to know more about this stuff than the YC people, who are scarily good at it but this is a significant departure from 'our goals are 100% aligned with those of the founders, what's good for them is good for us'.
I guess it's a question of whether on average YC is as good or better a post seed stage investor as the average VC who invests in YC companies. If YC is as good or better, then the pro rata is aligned with founders' interests since the founders are raising X dollars at Y valuation either way and it's just a question of which pocket the money comes from...it's still the same color.
In the universe of unicorns and rainbows, YC's participation puts the rest of a round's participants on their good behavior to reduce risk on future deal flows and the founders get a better deal. The situation in the universe with evil Spock is of course different, but it was going to turn out that way in that universe. In between a founder could probably ask YC not to participate. Since the investment is blind and YC is under scrutiny by potential founders, it may not be in YC's interest to force the issue and suffer Tweets of outrage.
The potential problem is a bad cap table and the first order issue is VC that treats that as an acceptable byproduct of a round it is leading or a company that does not have better options.
Yes, this is YC acting more like an investor and less like a founder-supporter which may turn into an interesting trend. However, I don't think pro-rata or participation rights are problematic as they encourage follow-on investment which is usually desirable. The downside to rights like this is a minor increase in the complexity of completing investment rounds.
