https://www.youtube.com/watch?v=pbFkw_roJqI
This is not a perfect analogy for investors and founders, but it is an example where supposedly incentives are aligned but in reality they might not be. What's best for the investor is not necessarily what's best for the founder.
But again, in this case I do agree that YC is providing useful advice.
Pro-rata is in theory the right (but not the obligation) to buy back in, at the new price, to get back to your prior ownership level.
In practice however, pro-rata is a firmly stated polite request to the next round lead investor to let you do so. The real determinant of whether you get to use the pro-rata right is whether your next round lead investor is OK with it (and whether you want to try to block that next round).