The short answer is no.
You can either have them available as controls (and under MOD control) or the plugin itself can respond to MIDI-CC. You cannot have both.
Say you send a MIDI-CC to move a drawbar and at the same time move a control. There’s a conflict. Who would win? The technical reason: A plugin cannot modify its own inputs (ie. receive CC and set a control-input which is under host’s control).
The proper solution for this would be to allow a MOD-GUI to send/receive MIDI-CC to control the backend. This is not yet possible with official MOD (There’s a prototype for LV2 Atom communication which will eventually allow this, someday).
Likewise the current MOD does not yet allow upload of files via the web-interface…
Meanwhile you can probably copy config giles manually to
modduo.local:/root/.config/setBfree/default.pgm (after creating the folder
~/.config/setBfree/ on the MOD.
There are already about 32 /normal/ controls (drabars + switches) binding those via MOD to CC per pedalboard would already be a PITA. – Furthermore setBfree has few million internal parameters. Exposing them all via control-parmeters would be plain mad.