I'm not all that experienced with email on Linux either but I believe that you have your concepts mixed up. I have managed email on Solaris and the concepts are the same so I may have some helpful information for you. Let's find out.
Dovecot is a mail transport agent (MTA) or mail server. It should not be looking into the home directory of a user account.
/var/spool/mail/$USER is the correct place for any mail transport agent to work in.
The user account mail in $HOME/Mail is managed by an email client such as Kmail. The email client talks to the MTA. The MTA manages the files going into and out of /var/spool/mail/$USER. The email client manages files going into and out of $HOME/Mail.
I hope this helps.