The scene revert setting won't accomplish this. There's no way to have your most recent choice in one scene maintained in the next scene without doing some additional setup work.
Alright, I'm in the manual. So to accomplish this, I would take cc# 16 for external 1. Then change the cc#s for the parameters I want to change to 16 on the axe? Wouldn't that assign to the expression pedal and not the MFC? And what exactly do I do on the MFC aside from setting the IA switch to none? If I do this on one preset, will it also be like this on all the other presets? Like setting an IA to X and that is its function for all presets? Or will it just be like this for this preset? Sorry this is really confusing to me.
Choose any of the other 11 Ext Ctrls. Note the CC#, like Ext Ctrl 2 = CC#17. Set the desired XY functions to the same CC#. Once the switch is configured on the MFC it will control those XY functions in every preset. Ext Ctrl 2 is what can be assigned per preset to bypass blocks in different ways or do other things.
If your presets are consistent enough you might be able to skip the Ext Ctrl part of this. Say you set all amp & drive XYs plus GEQ1 bypass to the same CC#, then set GEQ2 bypass to a different CC#. A general use MFC IA switch can have 2 CC#s (actually more but 2 that are easy to program) and off/on values can be anything, like 0/127 for one CC# and 127/0 for the other. That means by choosing one CC# or the other for these functions in the Axe menu, you can decide whether a block is in X or Y state and engaged or bypassed when the switch is on. Turning the switch on (or off if you prefer) would go from Y to X on all of those blocks, engage GEQ1 and bypass GEQ2 at the same time.
MFC Manual section 12.4.8 describes how to configure general use CCs.
On the first screen you'd want to see something like
IA06 c1 CC#017 Ch01
The "017" is the key part there, IA# will be whichever switch you're configuring, Channel should match Axe channel which is 1 by default.
Then on the screen with values set:
Off000 On127
For the opposite-bypass blocks repeat process for the IA's c2 using the other CC#, with Off127 On000.
You could optionally set an Ext Ctrl to one of those CC#s anyway. That will let you override the usual bypass action with a bypass modifier, per preset.