What about this from the Best Practices Guide: “A good font manager will recognize the need to use different versions of these system fonts and correctly handle the activation for you.”
It implies that a good font manager will handle any conflicts.
It also says: Since the OS must have some version of these fonts active in order to run properly, it can be difficult to disable them in favor of other versions. It can be done manually, but this requires some modifications to your OS that, if done incorrectly, could leave your system unusable.
Your suggestion worked for me for about 5 minutes. Then the boxes with the question marks came back. So, either my font caches are becoming out of sync immediately or it’s something else.
Does anyone else have this problem with Sierra? We can’t be the only ones. It was happening occasionally with earlier systems but never this bad.