XC_Bags is mostly about convenience and not rebalancing. And I tried to remove a couple of inconsitencies. (For example making poison stuff do a percentage of damage instead of fixed damage seemed natural to me because they are the healing equivalent of healing potions for zombies, and regular healing potions also heal percentages. Stuff like cleaning up trader's inventories is convenience and nothing else. Cleaning up some treasure tables came from my paranoia about out-of-handles crashes, I had 2 unfixable crashes in my first 2 attempts to play EE unmodded ;-)

Since there has been no negative written feedback lately, the mod seems kinda stable now after many bugfixes. (Some minor 'bugs' are still there but are hard or impossible to fix in existing games and are not game breaking and my 'Divinity motivation' is currently somewhere below the basement.)

Personally I would not recommend a mod for a first playthrough. Maybe you decide to give the game a second try after a first unmodded playthrough. And then choose one of the mods that seems most interesting to you. Better Logistics seems to have the least changes to the unmodded game, but I haven't personally tested it. Same with Scales, I only downloaded that recently myself, because it required registration with Nexus which I tried to avoid for a long time. So I only know as much about it that you know, that is the info in the Readme.

If you are interested in modding yourself, which your initial post suggests, you can look into all of them yourself and find out how things are done.

I have posted a data sheet a while ago which also has damage values. I found out that spell damage uses a very similar formula to weapon damage. I would not manipuilate spell damage too much because it seems pretty much in line with weapon damages. If anything I'd play around with cooldowns and AP cost.
You can take a look at the file Public\Stats\Generated\Structure\Modifiers.txt in the section 'modifier type "SkillData"' to find out what can be modified with spells. Not everything affects every spell type ("Shout", "Target", "Projectile", etc.)

Here is the data sheet, it's LibreOffice format:
A data collection for stats