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The phrase that jumps to mind is "Easy come, easy go".

Companies built on slow painful progress inevitably have a broad customer base, customers that were acquired through slow painful progress (although they probably have a few whales still). They're less likely to have the loss of one deal/customer sink the whole ship.

The problem with "big deals" is the shift in focus required to even have a shot at getting one. It's not so much "problems encountered", it's that there's no way to maintain focus or vision before or after the big deal. If your focus itself is big deals, then this doesn't apply.

But most startups have to focus on the product and that's hard to do when dealing with a large company who's priorities are generally misaligned with the broader market's values.

It's not a big deal as described in the article. The effort to apply to YC is nominal, not terribly distracting, and probably a good exercise even if you don't get accepted.