"Is there a way for them to be distinct stompboxes ( sending different CC values than those on patch 00  )?"

No. You would need to go to UNO2 for that.

It's possible to set up the stock chip (or UNO in stock mode) to do that, but it severely limits the number of Banks/Presets you'd be able to use, and you lose the ability to track the LED ON/OFF status, as you'd be using simple presets instead of the UNO features.