Hey William,
Server Templates are
the only supported way to alter just about anything in your configuration. It's definitely not a hack, and it is the "best practices" way to do just anything configuration related in Virtualmin.
On the other hand: user@domain.com usernames
are a hack, and are a hack on any system--not just ours--but we do support it and will fix any problems you run into with this type of username...we're just the only folks who are telling you that this type of username can cause problems with some software. I believe all issues with this kind of name have been resolved on Virtualmin systems, but I could be wrong. Newer version of cyrus-sasl require a configuration change that isn't automatic in our installer (yet), but it is documented in the FAQ. So, it isn't a "bad" practice in the sense that we won't support it or that anything Virtualmin does won't work with it, but it could cause problems with some software (not ours, but there is a lot of software out there that deals with mail and mailboxes).
You're definitely not alone in being intimidated by Server Templates. For some reason, they are viewed as very intimidating things to change--but that's exactly why they exist. It's so you can create "plans" with different types of features and options (larger or smaller quotas, more or less databases, more or less mailboxes, etc., though it goes far beyond mere "plans" as supported by other control panels...which is why we've named it something different) without having to specify it manually every time you create a new domain. If I can figure out why folks don't want to change Server Templates, we'll try to fix it--it's obviously something seriously wrong in the way we're presenting them in the GUI, but I'm not sure exactly what. Is it just the name? Would a Server Templates guide help?
Anyway, here's the FAQ on @ in usernames, which I believe covers everything you need to know about supporting them on your Virtualmin system:
http://www.virtualmin.com/faq/one-faq?faq_id=1511#51230