I’m reading your 1st question differently than Martin.
When you create any Input or Output channel it should appear inside the I/O Folder when shown in the Project Window. But most of the time (at least on my system) these new channels appear only in the MixConsole and not Project Window - for example they are not listed in the Visibility Inspector for the Project Window. For some mysterious reason these get shown in the Project Window only for automation data. In the MixConsole for these “missing” channels enable Write Automation and then disable both the Read and Write Automation buttons. Those channels will now be available in the Project Window. You don’t need to actually create any automation data - just enable/disable it. If you have a bunch of these Quick Link is useful. Remember to save as part of your Project Template(s).
Martin is right about question 2. But, since the displayed order is the same as the creation order, you can just delete all the current buses (save as a preset first) and recreate them in the desired order. A bit of busy work for sure, but you only need to do it once.
I just reconfigured all my Input Routing so I spent an hour or so doing this recently. Much more enjoyable than dealing with the physical cabling imo.