Do note that undo-tree not only provides a visual, it is a fundamentally different way of doing undos. The stock emacs way is not a tree, it’s a line. There’s no real “redo” in emacs for instance, you just undo an undo. It’s odd, but undo tree works really well.

I have recorded a video, it’s in the OP.

Ok, I just did. It’s (global-line-numbers-mode). Now… why??? It’s odd as hell.

I just tested, it reports that I’m dragging the mouse and setting a region, but it’s weird because if the issue is my clicking being sloppy, when it should happen in emacs with no config as well, and it doesn’t.

      ;; mouse-drag-region
                 ;; mouse-set-region

This is when I click and the button doesn’t get pressed.

   ;; mouse-drag-region
                   ;; Info-mouse-follow-nearest-node

And this is when it does register.

I can never reproduce the issue on emacs without config.

Nope! And when I tried with my config the very first click had that issue. It’s very weird tho, I have no idea what could be causing it…

Nope, vanilla emacs in that respect.