How about two edit boxes: The first one containing article text, and location-specific material (including pointers to references, links, images etc), and the second one containing meta data (reference bodies, categories, GPS coordinates...)
I don't like this (but I may be in the minority). Wouldn't it be simpler to implement template expansion inside ref tags in Cite?
Templates are expanded inside ref tags... enwiki has dozens of {{cite}} templates.
I'm not sure two edit boxes is a good idea, but some kind of <meta> tag (probably need a different name to avoid confusing with the HTML meta tag) which can contain all the meta info would be good. Keep it in the main source code, but separate from the content. It would make it very easy to modify section editing to allow the meta info to be edited separately to the rest of the page.
Nothing inbetween <meta> tags would be displayed on the page, which could simplify things like having to prefix links to categories with a colon to get them to display. If the category link is in the <meta> section, it would add the page to the category, if its anywhere else, it just displays a link (although that would break backwards compatibility, so might not be worth it).