There are two different things happening here. I’ll start with your second example, as that’s easier.
Most shopping carts, in your example WP-Ecommerce, create placeholder pages with a shortcode for things like the cart page and checkout page. All they’re doing to handle that is creating a shortcode function and inserting it on a page, then outputting whatever they need to in the shortcode function. In this case the shortcode is static, and there isn’t any other data being passed via the url. The actual product pages in WP-Ecommerce are just a WordPress custom post type with some extra meta data.
What you’re talking about, creating your own url structure via a plugin to pass data, involves writing your own rewrite rules via the WP_Rewrite class and inserting your own query vars.
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