I am sure you can't run MF 2.x on MF 3.0's firmware. But, the mixer should update the firmware to the attached app. (Wireless or docked.) So if the mixer updated to MF 3's firmware, attaching an ipad with MF 2.x should make the mixer update to MF 2.x's firmware. That is why you can't run both at the same time. If you are using My Fader for monitor mixes, you need to stay at MF 2.x Mackie is hoping to My Fader 3.0 out before the end of the year, but there are no guarantees. (For those involved in software development, this is pretty normal.) Considering how well MF 3.0 came out, let them go for it and get it right.
Firmware. We're used to thinking about the Bios update on a computer. In the case of this mixer, I'm pretty sure that the firmware is actually the mixer's custom operating system and program.