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Sure, you can make changes directly to the Apache config file(s).
Also, from Virtualmin, you can go into Services -> Configure Website to edit directives specific to it.
Or to edit any part of the Apache config, you can go into Webmin -> Servers -> Apache Website -> Global Configuration.
-Eric
Webmin is really quite clever when it comes to parsing config files. It parses what it understands, presents it in its edit boxes, and leaves the rest untouched when modifying the file.
So yes, Eric is quite right. :)
Though while in this case it should be no problem, you should pay attention when you plan to manually edit other things. There might be some that can cause trouble when doing it behind Virtualmin's back, e.g. directly editing a virtual server owner Webmin user account.