I like what you do here Falott and I think you're making great progress. I wish I had all the technical knowledge to answer all of your questions, but the truth is I don't.
However I have incorporated into my workflow the following when scaling in negative X (ie duplicating/mirroring).
Always freeze transformation immediately to keep things clean. If I want pivot back at origin 0,0 also a reset transformations immediately after. This is perhaps not so good for animation purposes and more in modeling
But by all means clean up all you can with Freeze Transformations.
Supposedly there are some tricks to prevent the rotations and joints to go the wrong way with some preparations but I am not experienced enough I'm afraid.
Maybe the answer is in locators? read up on them and see if it helps. Try something like FT, set up a locator in 45 degrees (like arms in half T split), parent joint to locator and see if it helps clean up things faster. Just a wild shot.