From Cliff's announcement, the only "incompatability" is the screens will be a little different. If you make sure your firmware stays on the same versions, you shouldn't have any problems with the sounds or interface changes, which is all something you'd have to do anyways. I doubt Cliff is actively programming two or more code bases... he likely has build options to integrate a certain hardware libraries when building different versions of Mark I/II, XL, XL+.
When products get designated End of Life by component manufacturers, that doesn't always mean there are suddenly no more, or even that they've stopped producing them. It typically means that if you have relatively new products or products in development, that you need to find an alternative. It's not uncommon for manufacturers to continue producing EOL components for some time as they wind down manufacturing on it. There's usually a phase-out time frame.
In relation to the Axe, it could mean, that there are enough out there to last the planned life-cycle of Axe-FX II mark II (which could be many months or years), but not enough to last the planned product life-cycle of the XL (which could be longer due to hypothetical new products either downgrading the XL+ or taking the same space of the mark II). Alternatively, it could mean there are enough mark II's stocked and built for the time being that it doesn't need a change right now, and we might see a Mark II+ in the coming months, but is not necessary as of right now.