Bypassed Loopers + Morningstar MC6

Hi, im new to Midi, like most i imagine.
My current rig has a very simple 6 loop programmable looper which for me is still the most useful thing on my board, I have half my board midi-capable pedals, the rest not.

Ive just ordered an MC6 to flick through presets on the fly on a couple of my midi pedals but im now thinking of redoing the whole board with midi and getting an ML5 for the non-midi pedals. The question i have here is obviously I can run my board with the audio signal going through all my midi pedals and then the non-midi ones can go into the ML5’s send/returns, however I really like how my current looper bypasses all the pedals and im wondering if it will effect anything if I plug ALL my pedals into 2x ML5’s (including the midi ones) so that they are all isolated and my audio signal doesnt flow through the midi ones before the output, would this cause any problems in the programming stage if my midi capable pedals are plugged into an ML5? The main reason is that it negates failure in a live set up, if a pedal/cable goes down it doesnt take the whole rig with it.

With this in mind, if I have 2x ML5’s and an MC6 I can theoretically with a single button push, change presets on pedals and engage/disengage whichever pedals i’d like rather than the current scenario on my board whereby i have a simple 6loop programmable looper so i’d have to change preset with the MC6 (one button press) and then engage the desired loop on the programmable looper (a second button press)

Thanks in advance!