Presently, Glyphs marks layers with differing components as incompatible. (Even if they have compatible outlines, for example if one master uses a four-node circle /bullet as a component and the other uses a four-node circle /period.)
However, corner components (and I assume caps) are different: if different corners are used in different layers, there’s no indication that the compatibility is off.
I would find it useful if the program would also signal those incompatibilities too.