Can I create a colour scheme for a custom chapter and the apply it to other chapters?
You can honestly play the game with unpainted miniatures, nothing prevents you from using your own color schemes, and many people do, though if you intend to be using these forces together in a mixed imperial army, it's best your color scheme between the different subgroups of your army is clear, so effects don't accidentally get applied to a unit from the wrong arm of the Imperium of Man.

Coloring a Mechanicus unit the Yellow and Black of your Imperial Fists could cause you to accidentally apply First Captain Lysander's Icon of Obstinacy to them, when it only applies to his own chapter's units.