Bypass with EXP AND Scenes

I currently use EXP2 to bypass a wah block with my Expression toe switch.
However, I found that this is actually very limiting because now that it’s assigned to a toe switch, I can’t use stomps/scenes to bypass it. There needs to be a way to use both scenes and EXP to be able to turn a block off/on, rather than only one or the other.
I’m sure many other users have come across this issue and have been limited to using two blocks, inverting their bypass state.

My QC is desktop and all footswitching is done on a Nektar Pacer foor controller.

I have a Mission Engineering pedal Out 1 into QC Exp 1 as the WaH and as a Control for a Volume block with the ME Out 2 toe switch going to the FS1 input on the Pacer.

I use two scenes each assigned to a switch on the top row of my Pacer. The first has the WaH off and Vol on the second is a copy of the first with the WaH on and the Vol off. The switch on the ME goes into the Pacer and has two commands that operate in sequence and flips between the two scenes. For instance if they gave us a dedicated cc# to turn any WaH or just assignable to a pedal in a preset to we could issue a direct command to it without having to take up a scene or a stomp button on the QC.

That frees up the other Exp pedal on the QC which I have a Zoom exp pedal hooked up that I assign to control gain either on a pedal or on the amp so I can go from clean to a little hair (or more hair) in a the preset.

This seems to give me the most flexibility until we get some more midi capabilities as we should all be lobbying for.

I also noticed that when I have my wah set to “auto-bypass when in heel position” it locks me out of assigning the bypass setting based on scenes. It is very limiting that I can’t bypass my wah completely when I switch scenes to use my expression pedal to control a different block.

I can’t turn off the “auto-bypass when in heel position” on my wah because I don’t want the wah to impact my tone when I am not actively using it. Because of this, my expression pedal is stuck on the wah in every scene.