Hey, thanks for the suggestions, sorry for the late response, but better late than never :F
1st, Schall Transport Group compatibility implemented! It's not perfect (see release notes), but better than nothing. Let me know how it works for you. I'll have a look at the Assault Spidertron and Aircraft mods another day.
2nd, implemented as a startup setting!
3rd, the zones are already in a separate group provided by that mod (and only appear when selecting signals or using the dedicated zone tool), so you should already be good to go here.