The “Inbox” file contains just the messages in the inbox. So it should be flat. The “Inbox.sbd” folder contains the mailboxes that are inside the inbox. So it should produce a hierarchy (that excludes the top-level inbox messages). Based on your above description, it sounds like the import is functioning properly.
In order to import both the messages and mailboxes in Thunderbird’s inbox, you’ll need to import both “Inbox” and “Inbox.sbd”.
If the “Inbox” file contains messages from one of the submailboxes, you may need to have Thunderbird compact it (using File > Compact Folders) so that it removes from the file the messages that are no longer in that mailbox.