This can be avoided with a midi controller that can send bypass commands based on profiles. I've done this That way I have 20 scenes on the Ultra (that number could be bigger, it's only limited by the amount of memory of the Arduino I used for the thing)
That would be multiple bypass and unbypass commands per switch press, cool, with additional expensive hardware unless you DIY etc,.
The Axe II/III/AX8 (AX8 has much less CPU vs the II, and way less than a III) has Scenes built in among all of the other advantages I mentioned above, with perhaps the biggest being it sounds a whole bunch "realer".
Congrats if you built your own DIY controller to alleviate the issue with the Gen 1 Axe's, awesome!