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I can't imagine why any CMS would be designed that way or, why, from a coding standpoint, it would be hard to remove. I try not to second-guess third-party providers (because I've been in their shoes), but that sounds like borderline BS to me. "Can't fix it" is far too often "Don't want to fix it". My gut feeling is that Google will ignore a standard port 80, and will only index the port if it's non-default or if the entire site (including internal links) is explicitly using the port. By adding that canonical, though, you're definitely sending a mixed signal, and there is risk. I've never seen this actual situation in play, so I can only speculate. Is it possible to remove the canonical tags on these pages and using 301-redirects or some other approach? Unfortunately, a lot of this depends on how the pages actually resolve and what other signals are in play. It's a bit tough to tell without looking at the specific site.

I'd worry mostly about it becoming a duplicate content nightmare. It would be better to have a choice to buy the brand new item or a refurbished one on a single product page. Think of how Amazon lets you select different versions of a books, movie, etc., different sellers, new/used, etc., all on one page.