Some servers store all folders as subfolders of INBOX, e.g. the Drafts folder is INBOX/Drafts. This is a technical thing that users should not see preferably.
On one such account
isync/mbysnc with a minimal config of
MaildirStore imaptest-local SubFolders Verbatim Path ~/.mail/imaptest/ Inbox ~/.mail/imaptest/INBOX Channel imaptest-folders Far :imaptest-remote: Near :imaptest-local: Patterns *
will create a "flat" structure (if you don't specify the
Inbox path then your Inbox will go to
~/Maildir and all the other folders will go to
~/.mail/imaptest and any further nesting is done as expected). I do not know how isync knows this. Maybe it automatically flattens any subfolder within inbox?