Please don’t do that since you may damage both devices!!!
The RJ45 is not a normal Ethernet port to connect to a network. The connector is simply up-used by MOD devices in the control chain protocol.
Everything that you mentioned seems quite easy to fix using Program Change messages to swap pedalboards and/or snapshots.
I use it myself on my live setup between a MOD Dwarf (used for guitar-based stuff) and a MOD Duo X (mostly for synths). Basically, I use the Infamous MINDI on the Master device (I use the MOD Dwarf in my case), sending the Program Change messages required to swap pedalboard or snapshots on the MOD Duo X (my slave device).
Wouldn’t that work for you as well?