As has been reported by other users: Apple’s own hardware yields the exact same results. Including using the build-in keyboard of a MacBook. It’s not just mouse shortcuts but Apple’s own build-in MacBook keyboards too, as has been posted.
I use an Apple keyboard too. Same issue: when I map specific keys to Mission Control actions they stop working after a reboot. The shortcuts are reset to the default settings by the OS. Only on Sequoia.
In other words this happens when using Apple’s own hardware and peripherals.
There is a bug in the latest version of the OS. Bugs happen all the time. Nothing new. They are Apple’s responsibility.
On top of that every other mouse I and other users have tested yields the exact same results. If you can no longer use any third party peripheral, including the major suppliers (Logitech; HP; …), then yes, there is a problem Apple should have a look at.
Oh, and that it can take a long time is not new to me. When Apple broke their own Apple Movie Store service on their own Mac mini 2012 using their own Apple monitor (black screen: no visuals, only audio) we had to wait for at least half a year before they fixed that bug. And yes: it was their own OS breaking their own service on their own hardware. They fixed it, but it took a long time.
As a user of Apple computers and devices since 1995 and as an IT System Engineer I have witnessed this many times both on my own devices and on our customers devices.
“It just works” is unfortunately not always true.
[Edited by Moderator]