After a bit of searching, I could not find Maildir support in Alpine although it does support IMAP over SSL nicely as did Pine.
I found it was as simple as checking that ssh via key (as apposed to user/pass aauthentication) was working to the mail server. If you have not already, set up your authorized key on the server.
Then setting the Alpine inbox to your server's hostname example.com
chris@server:~$ ssh server /usr/sbin/dovecot --exec-mail imap
* PREAUTH ...CUT... Logged in as [YOU]