I think I worked it out. I neeeded to change this setting to Stomp 8? I think that's working!
For anyone else looking at the thread, going into Global Settings -> Footswitches there is an option called FS8 Function. The choices are ToggleEXP (which is default), then AllBypass, SnpshtDn, SnpshtUp, PresetDn, PresetUp, Bank Dn, Bank Up, Stomp 8, TAP/Tunr.
Stomp 8 turns it the footswitch on the MIssion into "just another button", rather than one which switches between EXP1 and EXP2. You can then assign the bypass options on both blocks to Footswitch 8. Then assign the EXP1 to BOTH positions on the wah and the volume pedal.
This means that when you move the wah position, it moves BOTH the position of the volume block and the wah block, but if you set those blocks so one is on and the other is off, pressing the mission footswitch swaps which is active!
NICE!
This means, that if you've a snapshot where you want one effect to be active on the Mission, and another footswitch with a different one, you can just set the correct block to be active in the snapshot, and the mission will just control it properly.
I wonder why it doesn't work like this by default?