Hi,
I'm not sure to totally understand your problem.
If you have a category listing menu restricted to a specific category so the links will be:
/namekategory
/namekategory/1-nameitem
in the xmap sitemap.
I just tried on my local. If the products are reachable from different menus so yes, they will be displayed many times in the sitemap. So to avoid that, you can create different main menus, and select only one referencing the products in the options of xmap.
To improve the SEO another thing to use are the canonical urls, by this way when visiting your website, the google bots with take in account only the canonical url, so a unique one and not each url from the different menus.