Brian, there isn't a way to have them automatically come in on those separate layers, although that sounds like a good idea to put on the wishlist for future consideration to allow that level of pre-set-up. I'm thinking maybe an option with the division or subdivision in the RefNote Preferences.
I agree that in the division list would be the best place for such a setting.
But that's a lot of work to get them all assigned, not to mention the engineering which will also require some sort of report of all these division and sub-division settings to cross-check.
So I'm also curious what the end-goal is? Because depending on what your goal is, we might be able to just build that into the Highlight tool - for instance adding an F option to Freeze the selected block.