teddychan, the currency mod that you have enabled is not supported by XC SEO. you would have to modify the source code to enable support of that currency mod, or I can find an alternative solution for you when I have time
Miniature giant, i've been thinking about using SKU instead of ProductID for awhile now (and I lament the fact that I did not use skus originally...). you could actually replace the productid usage with the sku usage, which would reduce needless fluff in your rewritten url (i've found many users often search google using a sku, which would be better to have in your url than a productid)
Additionally, regarding your issue with urls in the javascript
:
#1. if I remember correctly, urls aren't being rewritten in the javascript, to prevent unforeseen issues with the myriad javascript functions in x-cart
#2. when a user visits your product.php url, they are being 301-redirected to the proper HTML url. I don't know about google specifically, but search engines typically do not have javascript enabled. even if they did, and if they visited the .php url, you might not gain points for pointing to a page deep in your site, but i don't see why you would get penalized for duplicate content, since a 301-redirect exists.
You would get penalized for duplicate content if XC SEO didn't redirect users from the product.php url
(which, btw, i believe the commercial xcart seo mods don't redirect from the old php urls, so their customers are starting to get penalized)