Probably won't be implemented in the tweaker, but you might want to try out T-Clock.

Which application has this issue?

Perhaps that's a duplicate of:

http://tweaker.userecho.com/topic/1050648-multiple-instances-of-edge-dont-have-an-icon-when-grouping-is-disabled/

I'm not sure about Classic Shell (you can ask its author) or the trackball, but 7+ Taskbar Tweaker shouldn't affect Aero Shake in any way. It works as expected for me on Windows 10, and I use 7+ Taskbar Tweaker with many options.

Looks like this is what you're looking for:

Do you have a way to reproduce the issue?

Also, please check whether the issue exists with older versions of 7+ Taskbar Tweaker.

You can get previous versions here:

https://www.dropbox.com/sh/mcbychsh0xc1dvu/8-Lj2sg3NP

You can do that if you enable one of the volume wheel scroll options.

I didn't understand what you mean. What do the volume settings have to do with with runtime priority?