Thanks for taking the time out of your day for such an in-depth review, much appreciated! if was my first time making a 3D game in Godot, so it was a fun learning process, I wanted to do something like this to avoid those pesky boned based animations in a 3D model.
I was wondering if the enemies in the physical dimension would end up being tougher. I think this might partly depend on the play though and how much of the level you have to clear in order to advance to the next. I didn't get a lot of time to work on balancing, but when I did, it seemed like the orb would spawn further away, meaning more enemies to clear, which turns into more enemies in Pandemonium.
The goal with the hit scan weapons for the normal enemies was to give it a more retro feel, but maybe I should dial back their damage or the timer for their shot. I kinda struggled with scoop creep, my intention was to only have 1 enemy per dimension, but thought trying to dodge both the melee enemies and the projectiles would be more fun then trying to just dodge the 1 slow enemy. The enemies speed and health scale up as well per level you complete, but guessing I had that tuned too low as well. Lesson learned for next time though, in a game like this, leave some time for balancing at the end.