No, they should produce the same result if the pages are the same. Do your local files link to the external third party cart? If they do then you will likely start crawling that site again as well unless you choose to make a site map of specific pages that you choose.
There are other ways to limit the pages, do you know if the type of pages your cart uses are different from the other pages types in your site? For example, if your site has .php pages and the shopping cart has .aspx pages then you could tell surveyor to ignore the .aspx pages. Also under the links to follow section you can specify how many levels deep the pages will be crawled. These settings might help you limit the size of the site that Surveyor is crawling.