I strongly suspect that this has to do with attribution and shallow "data driven" choices - there is a heavy bias towards things that are easier to measure. Especially in startups with limited resources.
Measuring retained users regardless of anonymous/known state is very hard and lossy. So the nearest easy to measure analog that is often picked is logged-in users and we start the fucked up cycle you mention.
Similar things happen around all metrics that have to do with retention. We know that a better experience through higher performance and better UX is likely to create happier users that return... but we cannot prove it (easily) so we focus on optimizing other things.
The number of users you lose by doing that is smaller than the number you gain as long as you don't have enough users (and spends enough on publicity). This is also the one thing that limits the number of users a company will ever have on most cases.
Fucked up incentive structures like this are why we cannot have nice things.