i use sup (which is where notmuch came from) because it provides on-the-fly virtual folders where emails match a search query or a tag. i can also open multiple folders at once and switch between them without loosing state. it's been a while, but when i last used mutt it could not do that
Coincidentally, I used to use sup and it is my favorite mail client that I've used. At the time there was no way to sync changes back to maildir or some format that IMAP could sync. Is that still the case?
https://neomutt.org/feature
https://github.com/neomutt/neomutt