I've done both equal and non-equal, but I've yet to have or observe a business where both the risk, contribution, and effort put in by the founders is actually equal.
Sometimes it's just a conversation founders want to avoid having because it's uncomfortable, but that in itself is a bit of a red flag.
I have no doubt you're right that it's frequently a red flag, and that founders often go equal to avoid ranking themselves.
I've also watched and been part of lots of partnerships where the expectation before hand was equal contribution, and the reality after the fact was lopsided. I feel fairly lucky that my most recent experience truly was equal risk and equal effort; my even split experience has been truly reflective of what's happened, and truly fair for both of us.
The big mistake I have made is giving people besides my co-founder too much equity. Nobody else who's contributed to my company so far other than my co-founder have lived up to what they said they'd do, and we gave out too much equity in advance of them doing it.
Considering that, and considering both the issue you brought up and the reasons YCombinator gives for pushing toward equality rather than away from it, I think the main thing founders need to do is have a mechanism for not committing equity in advance of the effort. It's important for founders to be on a vesting schedule so that when one stops contributing or contributes less for a long period of time, you can shut it off. And it's important to communicate that things are going off the rails, and then actually take the action to shut it off.
That's really basic and somewhat stating the obvious, but if you are diligent about cutting off people who don't contribute, then there's no reason to shy away from equal split plans in advance. My experience has been that people I've partnered with for equity aren't avoiding contribution maliciously, they simply and honestly didn't realize in advance that they don't have the time & energy they thought they did.
Sometimes it's just a conversation founders want to avoid having because it's uncomfortable, but that in itself is a bit of a red flag.