It took me some time to stumble over this mistake, but now I'm finally able to create new directories directly from neomutt and get them synched correctly to the IMAP-server. Since I use G-Mail right now that frees me from creating labels for everything since I can now freely move my mails through the directories and the sync will create the labels automatically. Btw. the default is mbox as stated in the docs. Reference: https://neomutt.org/guide/reference#3-243-%C2%A0mbox_type