So if I wanted to resell the product, can we rebrand the site customization per user, or role, or scope?
I think the short answer will be "no"...
Thirteetwenty is correct that you cant rebrand the site as a whole on a per user/client basis. What you could do though would be to have different Icons that are used on the client machines and also change the locations that the Agent Menu points to, although the core fucntionality around ticketing etc would have to remain constant.
So in the Agent Menu you could have a different About <ProductName> and point that to a different location for each customer. Not saying it would be easy to maintain but it would be do'able.