I am glad it helped you solving the problem.
Yes, configuring that realm on the server side is a possible alternative.
As for the folders, - not all people have multiple folders, and for those who have, not all folders need to be synced. E.g., for one of the accounts, I have over 500 folders. Many of them are sitting there for historic/archival reasons, so, that I could go back to one of them if/when needed, but those "projects" are closed. Besides, syncing 500 folders would bring my phone to its knees.
So, Aquamail doesn't link any other folders beyond the Inbox and a handful of other "special" ones.