the module Commerce product Url is for make unic urls based on product variations, it means when you have one product display showing different product variations.
Check this issue where they explain a little bit better what Im telling you
But there is a non-drupal solution to convert dinamic urls into SEO-friendly urls, that is using mod_rewrite:
Sad Original URL = site.com/node/1?id=54
Happy URL :) = site.com/node/1/rueben-sandwich/
Use mod_rewrite in your .htaccess file to parse out the elements of the URL. Like this:
RewriteEngine On //check that in drupal's .htaccess the rewrite engine is on by default
RewriteRule /(.*)/$ node/.*$?id=$1
(.*) pulls the element out and puts it in variable $1. and the
.*$ is just a wildcard that accepts everything after node/
Try it and tell us if it worked because I have not tried it with Drupal websites.
by the way, try to use sku, or some other argument in the url through the module configs, so your url would look better because using "id" the final result of the above code would be /node/1/54