From the docs I've just read about fetchmail, I don't use it myself but was curious, it seems that fetchmail acts as a kind of glue or bridge between two services. The first service being the remote POP3 or IMAP is pretty obvious. The second it is local mail delivery system which isn't so obvious.
Fetchmail grabs the remote mail and sends it to port 25 (the SMTP port) on the localhost. So whatever is listening to port 25 is where your solution is. On my Debian server there is exim4 there which can be configured I believe to do what you want. I had to switch this to Maildir delivery (opposite of what you are wanting if I read your post correctly) for use with IMAP so I could read email from any of my other systems.
I hope this points you in the right direction.
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