Hi Everett,
Thanks for your response.
I also believed that the rel=canonical merge the link profiles but so far all the evidence I've seen suggests that it doesn't.
Firstly - Jon Mueller from Google stated that the rel=canonical tag doesn't merge the link profile. That's talked about here.
http://moz.com/community/q/quick-rel-canonical-link-juice-question
Secondly, if I look at some examples, you'd expect pages with rel=canonical tags to have zero authority etc. reported for page alternatives in Open Site Explorer.
e.g. on the ASOS website there is a link to the men's section which uses a query string parameter.
http://www.asos.com/men/?via=top
The canonical url is
http://www.asos.com/men/
Both report different levels of authority. If the link profiles were merged, would you not expect either the same levels of authority reported or the non-canonical version to report no authority?
I understand that Moz tools don't work like Google so I'd like to hear from someone who can explain this.
Thanks,
Yusuf