If you want to run WIRES-X in Yaesu System Fusion Digital mode a FTM-100DR or FTM-400DR should be used. I have run for several months with the FTM-100DR and my repeater with the UDRC™ attached.
No special configuration of the repeater is required, other than having it pass the right mode (Analog or Digital). I run the repeater AUTO/AUTO. On the WIRES-X you have to pick analog or digital during setup.
As a side note, for stress testing, I ran the DR-1X with a FTM-100DR/WIRES-X in digital mode attached to "Americas Link" (the busiest english speaking room) and D-STAR attached to REF001C (the busiest reflector) and let them "fight it out" for weeks. The repeater never locked up and it switched appropriately depending on traffic source (RF has precedence). One would not do this in general practice, but it was an interesting test.
As you note, the node radio is set up with complimentary frequencies to the repeater, e.g. like a user station.
BTW, the Windows based WIRES-X software does seem to crash fairly often (daily?), so having the node where you can monitor and restart the program is an advantage.
73 de K7VE