I use the X/Y unconventionally - kind of the way you described at the beginning of this thread. I do it mainly to tighten up my presets. We play about 45 songs in a typical show, and some of the songs require up to five presets. I like to keep everything on one bank, and so.... You can probably use what I do below to get an idea of how you could make what you want to do work in Axe FX Mode (with some obvious trade-offs).
I have a dedicated "X/Y" switch on the MFC. I'm not looking at the list of CC#s, but I think "Amp 1 X/Y" is the first "X/Y" CC#. Again, not looking at the list, I'll pretend it's CC#100. I go on the Axe FX and change every "X/Y" CC# to 100. I assign CC#100 to that "X/Y" switch on the MFC. Now, everytime I press that switch, everything that can be switched by X/Y happens all at once. If I don't want an effect (or anything else for that matter) to change when I press that button - I just keep all of their parameters the same. I give up the ability to have multiple X/Y controllers on the MFC that are specific to certain blocks, but that doesn't effect me because I design each specific preset (or half of a preset now that I have X/Y) for each specific song. I only do this for songs that only require two specific tones, so I still have songs that take up 3, 4 or even 5 preset spots, but most songs are covered by 2 (clean and crunchy - usually).
Sorry if this doesn't come close to answering your question, but I love this flexibility - the way everyone can make this system work however they want. I'm probably just waxing poetic because my MFC is back in NH for repair and I miss it!