If a VC wants to own 20% at the end of an A, or 10% after a B, having YC in there with rights to buy back up to their 7% can add real dilution you wouldn't have otherwise wanted or needed to incur. As someone who did a party round seed and had a crowded A, it really does add up; though, it's for sure a first world problem and won't kill you, whereas YC for many companies is when they get serious.
YC is so valuable that this won't turn anyone off at the traditional YC early stage, but I wonder how this will affect things for the "late-early" companies they've been taking more of in the last few batches.