Is there some reason to believe that Y Combinator maintains "stances" on the 6,200-ish startups which have been through their program?
If not - since YC is a for-profit business, what paths to positive RoI might you foresee if they did maintain such stances?
Yes. Their reputation is taking on the reputation of projects they support. If they want to keep good reputation, they should watch over their sponsored projects.