Of course, you will need to have and use your own page-templates, not the ones from AtlasUI.
Yes you can. But I do wonder why you want to do so. Why not use Atlas as the base for your own CSS? Why trying to do it the hard way? You know you can easily customize the Atlas as groundwork and then add your own CSS?
Ok, thanks for the confirmation.
The reason for leaving Atlas is that all in all it does not cater that much gain for us, and I would like to strip it just out and replace it with a nice ITCSS setup that is lean and fit-for-purpose. Although Atlas is pretty robust in its setup it leaves us with a lot of redundant stuff, and just leaving it all together would fit out goal better.
I had have a discussion with Mendix about this but the answere from their side was not completely clear on this.
As your suggested approach @RonaldCartels they are suggesting to tweak Atlas but leave it in place. There was some talk about potential problems with support when leaving Atlas, but as @TimvanSteenbergen said; it is a separate module, and this should not have to weigh in on the matter.
Anyway, thanks again.