Unfortunately there is no currently a way to do so.
We have plans to add import settings to give more control over it.
Setting in asset tasks, to preserve material bindings - would allow that. We will pop a ticket with that task a bit higher.
Although this will only work if order and number of meshInstances has not been changed. Unfortunately there is no easy way to identify if meshInstances been re-ordered or changed, as there is no unique ID for them available. Meaning if you simply reorder meshInstances in modeling tool, and re-import, then you might have materials attached to wrong meshInstances. So that setting won’t be by default enabled, but will be available if you know that you want to preserve material bindings and meshInstances haven’t been changed.
Other option would be attempt to read and preserve meshInstances ID’s from FBX format, but this hasn’t been explored yet, to find out how stable those ID’s are.