I have a similar situation with a 16x08 as my primary interface. I also have a THR10, GT-001 and R24. The THR and GT can both be controlled/configured via USB while the 16x08 is selected, so I end up taking audio outs of these devices to record via the 16x08.
Unfortunately, there are features such as re-amping or even just getting dry tracks recorded that can't be done this way.
In the past I've asked that device configurations be made per project so that project templates could be created to make starting projects (and switching between them) with different devices really simple. I like your idea too, the only downside being that without per project device settings, opening a project created with one device preset while a different preset is selected would probably throw all of the I/O assignments hither & dither.
This would still be a step forward.