I typically have one PHP app installed per domain (or subdomain). Since sometime 2012 I have followed the practice of having one user per app and enabling Enhanced Security for each user.
Despite claims that Enhanced Security is enabled by default, it is not if you create the user as part of the "Manage Domains > Fully Hosted" set up. You have to remember each time to go and edit the user and manually select it.
Please fix this, Dreamhost.