I think you need to take another look at the script that reset's Baeloth's level in BG1. It hardly counts as a reset if he still comes in with 40k experience and all his spells.
Might I recommend amending the script to:
-get rid of every spell except two level 1 spells. I usually keep magic missile and identify when I'm resetting him in eekeeper
-maybe you can find the part of cdtweaks that determines level ups on join ("ToB style") and implement that to determine the experience he should have (otherwise, maybe give him 500. Because that's how much Edwin had the last time I picked up Baeloth. I'm the type of player that picks up my party member ASAP and then continues with the game. I know it isn't everyone's playstyle, thus my first suggestion)
-Also, the amount of spells he has "memorized" should be taken down to level 1: 5, level 2: 3, level 3: 3 (because of his ring giving him +3 spells for level 1-3)
-swap out the robe of the evil archmagi for a traveler's robe or something not so OP for a level 1. His ring can stay, since it's character-specific, even though it's OP too
-find the line in the script that determines your character has to be level 5 for him to trigger and set it to level 1
I don't know much about modding or I'd do this myself, so I recommend it here to someone who knows more
Otherwise, at least I don't have to deal with Neera guilt-tripping me because I don't want to recruit her (it's like "I'm sorry that I'm an evil party and you're annoying" XD). That alone makes this mod worth it.