1. I changed AllowOverride to All in /etc/apache2/sites-enabled/000-default to enable .htaccess
2. I ran a2enmod rewrite and a2enmod headers and restarted the apache2 service.
These changes did not seem to affect the mailserver since I had no problem to login to my inbox afterwards. Is it OK to do this?
It's fine.
Now when I have owncloud on the server, is it possible to integrate the calendar and files into roundcube just like it is on Kolab?
If you have related plugins for Roundcube, you can do it.
And finally, when everything is set up is it just enough to point my mx records from my domain registrar to DynDns to make the mail to work?
I'm not familiar with DynDNS, but if you're using a dynamic IP address (like ADSL), you'd better get a static IP address for mail server. Because most ISPs (like Gmail, Hotmail, Yahoo!, etc) blocks email sent from dynamic IP address.