Yeah, tricky! You might be able to do something similar to getting native messaging extensions to work on Flatpakked Firefox as described here: bugzilla.mozilla.org/show_bug.cgi?id=1621763#c5
Hmm, no sorry. All I can think of is that maybe Kdenlive itself is a flatpak version in which case it wouldn’t be allowed to run external programs like Glaxnimate (or Pinta). I guess in that case it requires some magic with Flatpak overrides.
Then in Kdenlive, go to Settings -> Configure Kdenlive -> Environment -> Standard Applications, change the one for editing animation to point to that script. Should work now. At least, it did for me!
I’ve been using Glaxnimate which integrates with Kdenlive. It’s a tool for animating SVG elements. It’s a bit clunky I find but it’s nice in that you can have shapes and text follow animation path with different time curves. It can be used directly from Kdenlive which is pretty cool.
As for other tips, one I use a lot is Timeline Preview Rendering. If you have a whole pile of effects, playing in the project monitor can become very choppy. With the prerendering, you can just render that section and it will play smooth while still allowing you do edit the audio.
Finally, for getting the footage from clips, I use I and O to set the start and end of a part of the clip I want and then with Ctrl+I I can create a zone that shows up in the Project bin. I use that a lot to get the fragments I want first and then build the fill timeline later.