I have no idea what the technical hurdles might be. Just speculation, but perhaps the XMT and RCV resources are shared in some way? I've thrown a lot of multiple MIDI messages at my PitchFactor at the same time. The display starts freaking out, but it never seems to show signs of any strain (in an audible sense). So maybe it's not that the 'Factors have maxed out the alloted "MIDI headroom"?
Otherwise, I really can't figure out the reasoning behind the unusual "XOR" design of the OUTPUT setting. It's either MIDI IN + MIDI THRU -or- MIDI OUT with MIDI IN defeated. Granted, MIDI IN and MIDI OUT remain isolated in most any device. But some devices allow you to add MIDI IN to MIDI OUT. Clock's still active, MIDI can be received IN, transmitted OUT, and passed on THRU, simultaneously. You don't lose any routing options.
I chalked it up to Eventide making a design decision that included elements of "user-proofing". Perhaps there are fewer TS calls if you consider limiting the options. It's a great scheme for multiple 'Factor pedals (only). One's the XMT master, and the other two or three 'Factors slave to it (and pass the "master" data THRU downstream). But if you add a controller (or another type of stompbox) … Let's face it: If you already have 3 or 4 'Factor pedals in your rig, you're GOING to have at least one more 'box in the signal chain.
Eventide seems open to practical suggestions. If there was enough demand, and it was technically possible, maybe a MIDI Merge option would be good one to consider. That would certainly open up more possibilities in the MIDI controller area. Bullet point for the sales pitch: "Now, total MIDI compatibility across ANY rig!". Sell more pedals to the Gear Acquisition Syndrome crowd (like some of us here). The other side of the coin is, "How many customers use MIDI – at all?"
Or, (being a hardware company), they could dongle that MIDI capability into a FactorControl pedal. 
