I think simply switching the default colour to be the Layer one and the opt key for Glyph colour would be more intuitive.
I think the tricky bit is in the naming, the way I see it, the current Glyph colour is more a Font colour (it’s applied to the specific glyph in all the Masters) while the Layer colour is more close to what the Glyph colour should do, keeping differences between Masters.
The Font View shows a specific Master so I would expect the main colour to be about that specific Master and not about something that is applied across all the Masters. (I hope it makes sense so far).
I use colours to mark different things, and I found that the most important ones, as shape progression in a similar way that Kostas is using, are layer related (I’m using the word layer here not to confuse even more my point, to keep the Glyphs naming, but what I mean is single master related).
These things they also are the first things I’d be marking. Master marking happens at a later stage, so I think it would make more sense to have that as half colour in the Font View rather than the Layer Colour, and to have Layer Colour as a primary way of marking.