I'm definitely not Zarafa user so I might be not 100% accurate with my explanation. Take it with a bit of salt...
When it comes to receive and deliver mail with Zentyal, there is one single (I mean common) MTA (Postfix) always used, with or without Zarafa.
If Zarafa is not used, then MDA relies on Procmail to deliver mails to /var/vmail/
domain/
user folder.
Then Dovecot is used as POP3/IMAP4 server providing access to mailbox. You can access it using Thunderbird.
In case you want/need to use "webmail", Roundcube is implementing Web based IMAP client connecting to Dovecot.
This is what I call "standard" mail design.
If Zarafa is used, then Postfix is still used but MDA (as far as I know) is not Procmail but Zarafa. Standard access to mailbox is supposed to be Outlook or Zarafa web interface (or Zarafa client).
Because some users have other POP3/IMAP4 clients, Zarafa is implementing POP3/IMAP listener so that you can access your mail with, e.g. Thunderbird.
However, if you read carefully above description, you will understand that you can't have both "standard" and Zarafa mail backbone. I'm not sure stopping Zarafa is enough to have Postfix conf changed (back) to Procmail. I'll let Zentyal team react on this.
I'm spending time explaining this at quite low level of detail because there is a lot of confusion with mail service and willingness to use Zarafa without clear understanding of what is does vs. what is doesn't, or, even worst, to swing between standard mail and Zarafa. Doable but not easy without clear technical understanding
I hope I'm clarifying the matter here, not adding more entropy