Site set up with mutiple sub domains
The approach you described is interesting and should actually work. Separate root folders would allow you to define the template folders individually (→ see Ben's answer on how to set this up), but it looks like that's not what you need and your subdomains are more part of one and the same site.

Even with multiple root and template folders you could still include shared template partials, but sharing CSS, JS and assets would be troublesome. But, then again, more easy to have these individually for each subdomain.