Like I said, it's not at all just a KM editor bug. It might require KM editor tweaks to improve the situation, and it might be related to MacOS changes to mouse operation.
However, these changes occurred with Sonoma, when I had to alter the acceleration and sensitivity settings very carefully, related specifically to scrolling, for apps such as Pro Tools, Adobe Premiere Pro, iZotope RX, and Ableton Live.
I use the app "SteerMouse" which allows me to use, quite similarly to what the OP of the post described, to control each app and it's scrolling using modifiers I choose. There -are- things that change outside of an app's design which are in the OS, and suddenly change a lot of apps. This was my experience, for sure.
The acceleration and sensitivity are major factors, when one is a few pixels in or out. Perhaps there can and should be a fix from the KM Editor side, but only because most users will not use SteerMouse and MacOS keeps changing the acceleration settings (which makes the pixels jump slightly more than they did previously, which I would bet is causing these perceived changes rather than a "bug").
In audio and video editing, specifically, there are LOTS of "scrollable regions within scrollable regions" such as values on knobs among arrays of tracks with scores of notes. Thus, it's -very- important where the mouse is exactly. In SteerMouse I had to totally eliminate acceleration (using modifiers) of the cursor while scrolling in many apps, but only after the update to Sonoma, which allowed me to not lose my mouse as much.
If the acceleration is randomly increased by MacOS versions, this happens again and again! And to emphasize again, there are so many mice to choose from, that's why I use an app that allows me to do things differently than the OS, the mouse, and other apps make me do.
I mostly go on at length here because others might have similar issues and shouldn't be confused that it's only a KM editor bug when it's a "scroll within scroll" thing for me in KM editor and a huge number of apps, and I have working experimental solution. I had to update Adobe Premiere 2023 to Adobe Premiere 2024, and recently to Adobe Premiere 2025. The fact that the scrolling was messed up again after forgetting rushed me to SteerMouse to copy over my cursor acceleration and sensitivity settings.