This (long-known) bug doesn’t seem to be related to Smart Shift. It still glitches like mad, both with my MX Master 3 and my M650, no matter my settings. Reliable scrolling is only possible with the trackpad.
In SoundSwitch, there are also scrolling issues when using a mouse and trackpad together, though here it doesn’t “sync” the last scroll position between moise and trackpad. Means, if you used your trackpad to quickly scroll down your fixture tracks (because with the mouse it is much slower) and then want to precisely select something with your mouse, it jumps back to the top again, which is very annoying. → this has been fixed recently, thank you!