Hello, i am glad this is being discussed.
Add to this issue that if you set in any given layer properties display color to Red and print color to black, only projections are displayed black in layout (live plan and section views in Hidden mode with print preview on) while sections are incorrectly displayed in Red, or any display color given.
Only workaround i found for this is to override for every layout the color settings, which is well…
Somehow this is not high on the bug list to solve.
I agree with the OP, as i have too suggested in any opportunity given, everything should be controlled by layers. It is IMHO the simplest and quickest way to work and make changes, without UI clutter (everything is in one place the layer manager and not in every style dialog, in multiple tabs for multiple styles you want to print and display in layout the same way) .
best
alex.