Coherence is not measureable in anyway I can conceive, but I can tell whether an audio system is sufficiently coherent or not by listening. Some of the artefacts of coherence are timing, clarity, intelligibility and seamless transition from one driver to the other. I don't have measures for those either.
Phase shifting is, as you say, normal with filters (mechanical and electrical in combination). But if the transfer function is not accurate (rarely so because of non-linear native FR), then the phase shift is not as expected either. The key to loudspeaker coherence is making sure the relative phase between driver pairs is constant (for odd-order) or zero (for even-order). When the relative phase varies within the crossover region, you lose coherence. This has nothing to do with the inability of loudspeakers to reproduce square waves, which can be attributed to their limited bandwidth.
James