Thanks for putting this info up. I only started using TBird today& the sort order was already getting annoying.
A quick note though. I made all the changes you suggested & restarted - Much better, except the behaviour on delete was weird.
I start at the top of my mail & work down through. With mail.delete_matches_sort_order=true, when I delete a message the focus goes back to one I've already read.
Changing this back to false made much more sense for me.
All the best,