I am using IMAP. I don't see this option that you're talking about. FWIW, all my custom folders loaded correctly. It is just that don't see that top bar[0], except for social and forums (my least used ones).
I also noticed something odd. I closed it and reopened and lost all the info. I didn't install from snap or apt because apt was providing version 92 so I installed manually. I do see ~/.thunderbird (no ~/.config) but seems odd that the info wasn't stored there. This is a big red flag. ~~I also can't find in the settings where to specify the storage location.~~ (found)
The idea to use special filter is a good one, but as others stated the 'top bar' isn't a real thing in email. Maybe some sort of IMAP extension, but it's a bit like asking how to put onenote into a Google doc - you might find some workaround but you are looking at two different things.
I don't use those folders, I also don't use a local email client these days...
I also noticed something odd. I closed it and reopened and lost all the info. I didn't install from snap or apt because apt was providing version 92 so I installed manually. I do see ~/.thunderbird (no ~/.config) but seems odd that the info wasn't stored there. This is a big red flag. ~~I also can't find in the settings where to specify the storage location.~~ (found)
[0] https://i.imgur.com/AbCEZSm.png