I had to deal even with the manual xorg in the past, because wacom tablet didn't work properly and was pretty much useless in the "default" mode, with wrong button bindings and wrong things enabled, that interfered with each other. But xorg is too hard and too fragile, so I eventually found a way to at least make it not interfere and gave up. Accepted the "default" mode, putting only couple of "xinput set-prop ..." lines into .xsessionrc.

It's always been a constant battle with ubuntu for me. I lost that battle, automated configuration to satisfy ubuntu and don't bother anymore, mostly by avoiding ubuntu ways as much as possible.