Working in the animation timeline myself, I’ve run into all the same issues you’re describing. Really it comes down to sitting down and learning when/why Krita decides to do what it does because it’s not immediately intuitive. It could definitely use a bit of a UX polish though with the generalized feedback of animators. Maybe a poll or survey or something.
Personally, my biggest issue is with the inability to know what exactly you’re drawing on without making a conscious effort to squint at the timeline. When animating, I’d say half the time I’m drawing on the wrong layer on accident which adds hours to my workflow.
The layer(s) you have selected and the keyframe(s) you have selected are completely separate.
For instance, which layer would I draw on if drew on the canvas right now? Can you tell at first glance?
Hint: The last thing I clicked on the timeline was the top layer on frame 14

The answer was the bottom layer frame 18
