Pretty much every CPanel hosting I've ever seen does it this way.
I have several of these, with multiple domains on each. In my case, I use a throwaway domain on the main account, and the domains I intend to actually use are the Add Ons. The first thing I do is put a robots.txt in the root (throwaway domain) telling Google to stay out of everything. So far, I haven't had a problem with them indexing off that, since there are no links involved.
If you're actually using your main domain, you can just add a disallow for those folders to the robots.txt, make sure no links to maindomainexample.com/folder exist, and use the canonical tag. Shouldn't be a problem.