Who holds issuances of common stock isn't generally something that will negatively affect a valuation.
The important bit is that they're in it just like the founders are -- if the founders get diluted, YC gets diluted. If the founders go broke, YC goes broke. If the founders make money on an exit, or a liquidity event, then so does YC.
You can argue all day long about 6% being 'greedy', or 'predatory' or whatever you like, but from what I understand, the value they add far exceeds the amount they take, and means that they're invested in your success.
What PG did with YC is LEGENDARY. He was the first and will go down in history as one of the most pivotal figures in the entrepreneurial economy. The best explanation I've heard on YC's value add (or TechStars, etc.), is that it's like bringing on another co-founder, which makes perfect sense - as does your explanation above.
Looking forward to seeing future entrepreneurs continue to benefit from great program's like YC, TechStars, MC, etc.