my view on auto (or the Icom near equivalent CI-V Transcieve mode) is that an application that requires it should switch it on and a application that doesn't should switch it off. That way any application that doesn't terminate gracefully will not be guilty of leaving things in a "broken" state.
BTW in the case of Icom CI-V Transcieve mode only a very small number of rigs even have the ability to turn it on or off via CAT commands, so in that case the user must adjust the rig from the menu.
Returning to the topic ;) I believe there is a more serious issue with band changing on some recent Yaesu rigs in that they store aerial and other selections with the band. This would be fine if telling the rig to QSY to another band by sending a change VFO frequency command was equivalent to changing the band on the rig front panel, but it is not. The Yaesu CAT language for these rigs includes an set band command or a band up/down command. I think many CAT applications, including a couple I work on, fail to use this command and therefore defeat a very useful feature of these rigs. So if this area is going to be looked at in Commander then maybe the sequence to QSY should be:
1) set band (using the BS; command or similar),
2) set mode,
3) set frequency.