"What I'm asking is if the stompox mode can be turned on or off per bank?"
While the Stompboxes can send any signal you want, they will always send the same signals, on the same MIDI Channels, in every Bank.
You can send NOTES, but if you want the CC messages also, they're going to send in EVERY Bank.
And the SAME NOTES (when assigned to Stompboxes) will send on every Bank.
BUT....suppose you select a Preset that doesn't REQUIRE CC control - IOW, the devices in that Preset aren't set to respond to CC#s. You would then have 10 Pedals available for NOTES, as the CCs would simply be ignored.
While NOTES assigned to Stomp boxes will always be the same 5 NOTES, the other 5 normal Preset pedals can be assigned different NOTES in each Bank.
Load up the attached sysex.
Bank 00 allows you to select one of 5 presets. The Stomps send CC#s 001-005, and also NOTES 010-014. No NOTES are sent on the lower Bank.
Bank 01 sends no PCs. The Stomps send CC#s 001-005 and also send NOTES 010-014. The Lower Row Preset pedals send NOTES 110-114.
Bank 02 works the same way, but the Lower Row sends NOTES 115-119.
Bank 03 works the same way, but the Lower Row sends NOTES 120-124.
ALL NOTES ALWAYS SEND ON MIDI CHANNEL 2. Everything else sends on Channel 1.
The MIDI Channel selections were totally random on my part, just to demonstrate how the MIDI Channel configuration in Global Settings works.
If you set some of the Presets called by Bank 00 Preset pedals to respond to CC#s but NOT NOTES, and some vice versa, that's how it should work.
*You don't need the UNO Chip to test this, just use the virtual FCB without attempting a connection.
Hope that helps.