In theory you could plug a RFTX1 into port 6 on a MRX2 and route all of your devices to RF/port 6 since the RFTX1 is a IR>RF translator. The problem would be that the MRF260 is going to receive the signal and output everything to one IR output.

What I've been rolling around in my head is this: Program a MSC400 and then a MX890 or whatever you have on hand as a wand remote to control the 400 with triggers on each of the keys. The set that MX890 to out IR instead of RF. Use that MX890 to teach those MSC400 triggers as IR codes to another device which you can then import into the iPad app.

iPad app sends triggers to the MRX2 which has all devices routed to port 6, the RFTX1. The RFX250 on the MSC400 receives those signals and executes the commands associated with those triggers.

It's pretty complicated but I think that would work.