Thank you for the suggestion but unfortunately it's not a fix for my specific situation. Audio busses are not related to MIDI ports. The automatic bus assignment will help control bus assignment when you create a new aux track. If you always wanted to keep the first 16 buses free you can set it so it will only auto-assign bus tracks starting at 17+. This affects how audio is routed, but midi is sent via ports/channels.
What I'm doing is sending midi to more than 16 channels to a single destination, so port 1 channels 1-16, port 2 channels 1-16, etc. When using an AU3 plugin, I can send midi to multiple ports in Logic, but those port assignments won't save with my track stacks. When I reload the instrument, it comes back with ALL the instruments set back to sending on port 1. I then have to go through each and every track and reset the port number which, for big projects with several hundred tracks, is a real momentum killer.
Oddly enough, the port settings DO seem to be preserved with templates, just not with track stacks saved in the library. It's helpful if I go into a project knowing what my setup will be, but most of the time I end up adding these things as I go along.