As I was toying with transform, I saw how it will effect underlays and overlays and sometimes you don't want it to effect every underlay and overlay attached to the atom.
My problem is described here but while I'm searching for a workaround I figured this could be made a feature.
I thought there could be a variable containing bit flags to disable a certain function like color, alpha, blend mode or transform. This way I can set the object before adding to overlays/underlays and add them without worrying about it later.
For example:
var/obj/o = new
o.icon = 'something.dmi'
o.disable_function = COLOR|TRANSFORM