The main pull-down application menus should be left well alone. There's a reason MS recommendeda standard approach. Once upon a time I had to use Lotus Notes and 123, which used their own menu system that was quite unlike the Windows standard and made switching between applications more confusing than it should have been.
I've also used custom-built software where the developer chose, for reasons unknown, not to stick to Windows hot keys, to break things like tabbing between data input fields, ignore the Windows API regarding right mouse button clicks and all sorts of strangeness. User friendly that approach is not.
As for the menus for assigning track inputs and outputs, I couldn't really care what colour they are. I'd much rather the development time was spent arranging for audio inputs to be shown in a better way than the confusing "left number1, right number 1, stereo number 1". Applying the way MIDI inputs can be named to audio ins and outs would be a more useful thing to change than the appearance of the menu,