Generally though, yeah, it's absolutely best not to rely on overall, because even if all the overalls were absolutely using the same scale in every way, like in regular OOTP, it would still be a pretty flawed way to evaluate players, because of how much the individual ratings matter and because the overall can sometimes create an appearance of there being a much bigger gap between players than there actually is.
In game terms, there's probably only a minor difference, if any discernible difference at all, between most guys rated say 82 overall and most guys rated 87 overall. Or whatever. Pick your own number gap
But because of how our brains work as humans, we process a gap like that as being much more important than it is in the reality of the scale used in-game.
Thing is, I don't know how we could ever change that, other than by scrapping the overalls completely, which I don't think would go over well at all with most players
And overall does still have its uses, even with its limitations. But it's best to be aware that it is only a shorthand that's limited at best, and to plan your team and lineups while taking that into account.