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Hey Rick,
We've never really thought much about multiple partitions, because your users then get twice (or some other multiple) the quota you specify, and you can't claim 2x the space or users will bump into it when their mailbox or data on the other partition tops 1x...it's confusing. Actually, I should say I've never really thought much about supporting quotas on multiple partitions, but Jamie probably has because he thinks of everything--and it may be a bug that group quotas only get setup on /.
That said, anything that is configurable should generally be configurable in a template, and if it isn't now it probably will be in some future version. Quotas on multiple partitions, however, seems like it would present more problems than solutions--I'd much rather keep the deployment simple and keep all user data on /home (except databases, which are not easily moved or chowned to usernames, unfortunately, and so can't be quota controlled). Wouldn't it be easier to layout the system in such a way that all user data goes into /home? Maildir or the symbolic link for mbox style spools described in the Virtualmin GPL setup docs takes care of mail. Everything else is easily moved to /home, with the minor issue of having to recompile Apache (or see the thread on SuExec issues for a little substitution hack to do something similar...though I'm not sure I like the idea of directly editing the binary rather than just rebuilding, even if it does seem correctly null-terminated).
Is there some reason for not keeping user data in /home on your system?
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