Some of these issues are a result of using Artisanal Reskins: Bob's Mods (it is not intended to be used with Nullius, but I know that people do, and Artisanal Reskins: Nullius doesn't have full feature coverage as yet).
The rest though are in work; custom colors should work (you're looking for the setting under Artisanal Reskins: Framework, not Artisanal Reskins: Library; at some point Bobs/Angels/etc will be migrated to use Framework).