You are correct in your assertion that, while DotNetNuke is capable of multi-portal installations, many of it's shortcomings excede the multiportal benefits.  At PowerDNN we generally recommend single installations in almost all cases.  Is this a main site that will take signups for the dree installations, then have a provisioning process that will bring up a DotNetNuke installation for the customer? If that is the case you can just have an architecture whereby the site and the database are local. As you expand you can just add a server.  The nice thing about this setup is that your database queries do not have to traverse the network stack, this can greatly improve performance. 

Now if you are doing these sites for free you might want to go with parent portals to cut your costs.  The things about DotNetNuke is that it is resource intensive and, consequently, expensive to run with an acceptible level of performance.  We have some nice tools at PowerDNN for optimizing DotNetNuke sites.  This has really helped us in curbing the amount of resources sql server requires when running DotNetNuke sites. 

Hope I could be of assistance to you.  If you knew a little bit more on how you plan to provision the sites I could probably help a little more.  I think you have a good idea though!