Using the KB macros within Redmine Issues are functional.
However, the email notification of the KB URL assumes the webroot. (I know, my terminology here is terrible, but the example is self-explanatory)
I.E. within Redmine itself (Issues), the KB link resolves to "http://redmine.fu.bar.org/knowledgebase/articles/20"
The link within the email notification resolves to "/knowledgebase/articles/20"