Is there a way for sub-servers/aliases to create their DNS records in the parent domains zone instead of creating a new zone if the parent zone already exists?
I know there is an option to do this if you’re using sub-domains, but as the help says enabling sub-domains is strongly discouraged and it sounds like the feature will be removed all together at some point down the road so I don’t want to turn that on.
No, that usage of the term "sub-domain" is intended to refer to sub-domain names. This is why we deprecated sub-domain account types–the word means too many things and just confuses the heck out of everybody. It seems I will never be able to stop regretting the addition of subdomain accounts to Virtualmin.
That said, there’s a bug in current Virtualmin that doesn’t apply this option to sub-servers. D’oh! It’ll be fixed in the next release.
But, the option you’re talking about is the right option. It is not intended to only apply to sub-domain accounts (and if you enable sub-domain accounts and ask questions about them I will hate you with a fiery passion). 