Hi Jeff,
We've experienced similar issues with the WebStore feature of mojoPortal. It wasn't really designed to sell physical products but rather music, by the album and the track. Thing of items as tracks and offers as albums. Knowing that might help you understand why it is the way it is but it probably isn't going to help you use it to sell physical products. We've put together some very nice solutions with the WebStore but you're right, you have to build a lot of HTML for each product. We've eased the site owners burden by using the "Content Templates" feature. You can see probably our best work with the WebStore at Paschi Dev.
With all of that said, nopCommerce is a great Open Source .NET e-commerce solution.
HTH,
Joe D.