I'm afraid MIDI is what MIDI is. Many people find it useful.
You have various issues here, all of which are have solutions.
1) The nature of MIDI is that an output is either OUT or THRU. A rack unit will have separate outputs, but space limitations prevent this on a smaller box. If you want to use a pedalboard or such to control multiple units in series you probably want to use THRU.
2) You can solve your pedal problem by connecting it to all Factors in parallel – trying to use the MIDI outputs from the pedals conflicts with your requirement in (1) above.
Another approach would be to use MIDI Merge boxes, which can overcome the OUT/THRU limitations, but add complexity and (modest) cost.