See, that's exactly why you're wrong. This wasn't a bad "design". If the fix required to rebuild the whole thing from scratch, then you would have a point and thinking about it "prematurely" would've been a good idea. In this case, both the fixes were bugs that could've been fixed after the game was finished without having to undo much of the work done.
The whole point of the saying is that you don't know what's gonna be a bottleneck until after. Yes by optimizing prematurely, you would've caught those two bugs early, but you would've also spent time analyzing a bunch of other things that didn't need to be analyzed. Whereas if you analyze it at the end once people complain about it being slow, you're only spending the minimum amount of time necessary on fixing the things that matter.
I think that we should also stop doing crash tests in cars. Just release the car to the public and analyze human crashes afterwards.
Premature optimization is about trying to optimize the micro (a given function), while you don't yet have the macro (the game itself). If the function accounts for 0.1% of the performance of the final game, it doesn't matter if you make it 5x faster since that will only make the game 0.08% faster. You could've spent that time optimizing a different function that accounts for 10% of the performance, and even optimizing that function by 5% would make the game 0.5% faster, which is more impactful.
That should be embarrassing for Rockstar but I don't think they would even notice.