XC SEO dynamically rewrites your urls, so you would be safe to move to the root directory.
Regarding the urls, XC SEO and DSEFU both include variables in the url in the pattern that you mentioned. Neither currently offer the ability to have a completely clean url.
While I do intend to release a completely custom url SEO module, the only solution at this time is to use CDSEO.
If you have any more questions, feel free to ask
-Jon