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'.
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.