Yeah, that sounds correct. Since the TF doesn't have a MIDI Merge function, you can't use the TF to transmit clock and another controller to transmit PC without adding a couple of external MIDI utlity devices.
You can do what you want, but you'll either need to not use your MIDI controller (which I'm kind of doubting is feasible in your rig) and use only the TF to transmit both PC and CLOCK, *or* find a way to add a CC from your pedalboard, *or* add some addtional boxes.
It's kind of like trying to hook 2 microphones into a single PA. You have to have some way of mixing the 2 mics (transmitting audio) before they enter the PA (receiving audio), basically need a mixer of some sort, and that's what a MIDI Merge does. Say you've got one mic that goes straight to the PA, but the second mike also feeds the stage monitor. To do that, you need a splitter, same with MIDI.
The idea of adding a MIDI Merge function to the Factor pedals has appeared several times. I'm not sure what doing so would technically involved, so I'm not sure if it's even feasible, but it would be nice. I'll be keeping my fingers crossed.
Anyway, I hope this at least helps makes sense of what you can do and what you can't in this situation. Please let me or anyone here on this forum if you have any more questions or would like some more information, ok? I'm sorry it wasn't exactly the answer you were looking for, but I hope it gave you a few ideas about how you could still work this into your system.