Yes, all data is tied to a site.
The WebStore does support products and order tracking and even some reports and charts. It does not yet support inventory tracking, vendors, or wish lists.
There are as far as I know no third party vendors selling ecommerce store functionality that is designed to be integrated with mojoPortal. Part of my strategy for making mojoPortal more popular is to continue improving the WebStore until it does support general purpose ecommerce scenarios and its advantage will be how well integrated it is.
Currently I'm the only one I know of selling third party add ons for mojoPortal in my Store. There are a growing number of vendors offering support and services around mojoPortal and I think there are ripe opportunities for third parties to develop add on features for mojoPortal and I hope to begin seeing some of the DotNetNuke module vendors port some of their products to mojoPortal.
I think the large community of third party module vendors is the only real advantage DotNetNuke has over mojoPortal. I do not think their platform is as nice to use or work with as mojoPortal. Many of the most popular add ons for DotNetNuke are for things we already have had built in for a long time like friendly urls and google analytics integration for example though I hear they are finally getting that in the new version.
My main criticisms of DotNetNuke are
1. It seems slow and it seems to consume a lot of server resources
2. Doesn't produce good markup. Its 2009 and DotNetNuke.com just now finally got their home page to validate against the w3c validator. Hard to find any other pages on their site that validates though.
3. Skinning is difficult
4. Accessibility is lacking, you cannot manage any aspect of a DotNetNuke site if javscript is disabled.
So they are bigger but I do not consider them better than mojoPortal.