I'm taking a quick glance at Din's Additionals -- just to see an example of skill modifications.
Yeah, what can be modified is hard-coded
It's not formulas in the game that we can simply modify on our own. Not that I can tell -- Shadow would have to confirm.
Skellys have one of the stats that's a "Per User Level" stat:
I'm trying to think whether anything other than things that are summoned have a "scale per user level" effect....so I can look at that skill in the files to see what is done about it -- but I can't think of any.