Adding virtualenv is definitely one more layer of complexity, however installing everything to site-packages is asking for a lot of trouble to new users that don't understand whats going on. As soon as they have multiple versions of a library from different projects they will be an a world of hurt that they're unaware of how to untangle themselves. Starting with virtualenv from the beginning really will help prevent a lot of headache later.

If you're using Flask now and use it later and have two various versions you essentially get 1 working application and 1 broken one due to versions.