I admit I'm no expert on how to publish your own feed for WebPI to pick up, but I know absolutely that you can create your own MSDeploy (Web Deployment Tool) packages of your non-public apps.
The apps that WebPI installs are packaged using MSDeploy - and if you don't mind not having the shiny UI you can use the MSDeploy (Web Deployment) tool to package your app and then have your customers install them using MSDeploy, as well. The packages are a .zip file that can easily be posted to a site/sent directly to your customers.
If you are interested in learning more about MSDeploy you could start with this introduction:
http://learn.iis.net/page.aspx/346/web-deployment-tool/
Or post questions on the forum: http://forums.iis.net/1144.aspx
If you want to learn about how to publish your own feed for WebPI, try posting to the WebPI forum: http://forums.iis.net/1155.aspx. You might see a quicker response from there.