this is exactly why i went to an Axe Ultra way back. my Roadster would pop during the gig when i changed channels.Man, I have been pretty happy with my switching, seems similar to my tube amps were (dual recto, tremoverb, and mark iv) they often had a pop sound when switching too.
changing sounds has always been an issue for musicians, especially guitarists. that's why line switchers exist, why pros use 4 of the same amp to change audio only for 4 different sounds, etc., leaving them on one channel the entire night. i guess many people don't realize this.
some less expensive digital gear that doesn't use as much CPU might change instantly, but it's because it's not working as hard as the Axe and other gear.
gaps or noise when changing channels isn't anything new. some don't have that experience, and that's ok. but believe some of us, many things have the same issue.
it's great to wish for faster switching of course. and as i've mentioned, Fractal will update the FM3 when possible to be as fast as it can. the Axe3 had a gap with Scenes, then they updated it to have no gap in most situations.