Right click on a mailbox -> Compact this folder

you're right but imagine you have many folders with non-expunged messages: You won't see them - so you won't have an idea where to compact folders.

Thunderbird offers a possibility to mark deleted messages.

And there's the problem back: The IMAP's semantics of "delete" are not the same as the one from most programs using a "trashcan".

The supposed behaviour is that a folder with messages marked with "\Deleted" should be expunged when a new folder is selected. This used to work before but something may have changed since then.

How it works is that once messages have been deleted, the folder IMAP url is saved in the user settings via -[SOGoMailFolder markForExpunge] (invoked from deleteUIDs:useTrashFolder:inContext:.