Yep. I think it’s most of the problem. See at [LH2754] Size of toolbar icons . The line-drawn icons in the main toolbar are dimmer when they’re enabled than those in the formatting toolbar are when they’re disabled. I think that’s just wrong, a miscommunication in the graphics specs.
By the rgb hex numbers, the main toolbar icon are #898989 when they’re enabled. A bit lighter than the formatting toolbar icons are when disabled, #7E7E7E.
At the other end, enabled formatting icons are near black at #444444, disabled main icons are barely visible and minimally differentiated from the enabled, at #9C9C9C.
Team Scrivener, please check for a specs goof. I can’t believe this was intentional. 
Rgds - Jerome