After years of being irritated by Mutt threading my messages by Subject and then sorting those threads by oldest message in them, I finally took the time to figure out how to get it doing what I want. As is often the case with Mutt all this info was widely available, it was just scattered or lost in huge examples of muttrc files.
set strict_threads # Don’t thread messages by Subject
set sort=threads # Sort messages into threads
set sort_aux=last-date-received # Order threads by most recent message