I've been in more product meetings that have uttered a phrase like "we will work out what to do with all these users later" than I care to count. It really is a startup goal to sign-up as many users as possible. In most cases it is literally a metric for the next funding round ("Last quarter we had 100k signups!" Is a very attractive soundbite at the round table)
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.