In the manual there is a warning that the switch will not change pickup selections when the charge drains enough, and the guitar will make no sound at all if it drains enough after that. Anyone using EMGs has in mind that the battery is essential, but those pickups take a long time to drain enough of the battery to degraded the tone. In this context I'm not at all into the idea of the switch being so dependant on the battery. I assumed if the battery were not in at all it would still work in the last way it was programmed (like maybe a watch battery would take over and maintain memory, or something like that). Knowing this, I have to echo the OP, and I just start to think of this as a point of failure only. I guess if the app lets you know battery status and warns you when to change, that's one thing. But you guys are also right that apps don't necessarily stay updated, usable, or even available, so this does not seem as future proof as it could be.
I think a good alternative is really to route and install enough physical switches to allow for every variation. Pain in the ass to navigate, but it would work in a future proof way. Binary tree switching can get you there too if you want to remove the pickup selector.
Awesome Guitars has solderless PCBs and pickguards for that, but I think even their implementation would be better if they integrated blade pickup selectors rather than just a row of mini switches. I prefer a blade selector plus mini switches for variety of I'm going that route.