We can only guess as to the reason. My guess was that it was necessary in order to implement their new push toward better modeling. If the dedicated looper/rhythm module as a global feature ate up a significant amount of resources across the board, then that's probably the answer.
Think about it: if the Looper is a global function, that means it is eating up resources whether you are using it or not, and possibly at the expense of much higher resolution modeling. If that's the case, then I'm perfectly fine with this decision. That may be the ONLY explanation that would make sense to me.
Of course, I don't use the looper but rarely, so I don't feel the pain. I would say that if I were to be into looping, I'd likely use some other outboard looper if it were a huge part of my performances or an important songwriting tool.
This is why I sort of feel like the B3n isn't a great choice for those looking for a wildly flexible all-in-one pedal. However, a B3n combined with another multi-fx is a pretty potent combination IMO, and budget friendly, too.