If you really want to, that'll work. You may specify the directory when creating your Fully Hosted (sub)domain.
I like the addition of the "www" subdirectory, as it somewhat mimics the Logs directory.
In my case, each Domain I create belongs to a separate User, so the domains aren't all in the same directory, and easier to hand off management responsibilities.
If you prefer that all of your domains belong to one user, then your setup is very manageable and clean. In some cases, you may have to create a ~/www/domain1/data_dir/ folder for data you don't want to have in your web space.