Yes, you can host it on your own server without losing functionality.

Also, with Dotcombuilder, you don't get to download any zip files.. you are forced to install a site using their installer, which means that if you are forced into constantly renewing in order to create/install/sell additional websites once your membership is up.

Prozilla lets you download the zip files but their sites are awful, the scripts are buggy and most don't work.. Their customer support is next to none and they rarely ever update anything.