I think the problem is wanting two skills to do the same thing, that is incompatible with the skills system. Now two skills that interact with a tool in two different ways, now that's more like it (no need for a complete system overhaul).
What I would propose is that, people with artistry when using make-up just give you specific make-up: Eyes, lips, etc. This does not disguise you.
However, if you use the disguise skill with the make-up, you get a general (and none traditional) make-up that effectively disguises your appearance.
(You just add two different commands to the tool, for two different functions)