Taxonomy and primary links

I was hoping someone with a little more experience maybe able to help explain the best practice relationship between taxonomy and primary links.

Suppose you have a site (a newspaper/ magazine) with the following categories (there will be children of these categories too):
News | Politics | Sport | Entertainment | Business

and three geographies:
USA | Asia | Europe | Africa

Now it is pretty straight forward that you'll have two vocabularies. One, "topic" for to classify the content according to whether it is News, Politics, Sport, Entertainment ... and two, "region" for the appropriate region.

Question: What is the best way to select your primary links?

Should you link your primary links just to one of the vocabularies or doesn't it matter. In this instance I'd imagine that it makes sense to have "topic" as your primary link.

Okay, suppose you decide to mix the primary links between "topics" and "regions" then the designer faces a problem. If a node cuts across two of the "primary links" and you want to highlight and active-trail how do you decide which to highlight? Or do you simply highlight both? Question: What is the best way to handle this?

The latter solution feels messy. I think you'd only want to highlight one category ... therefore I think, for this type of newspaper website, mixing vocabularies as primary links is wrong.

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