You're right that I've never read the 2e and 3e sourcebooks, just 5e and some OSR stuff, but nothing in between.

Most of my experience playing DnD comes from playing in homebrew settings. Maybe the real problem in that case comes from trying to use a roleplaying system that has a bunch of cosmology and mysticism baked into it in a setting that either lacks that or has metaphysics that actively clash with it.

But if so I think that's probably a pretty common experience with how 5e is played.