The square footage is probably less because you're almost a townhome with the shared wall and roof. It can be a riskier buy because the other owner could make things difficult for you. My mother lives in a duplex, and in the last few years the building needed a new roof and tenting for termites, both of which would have been huge hassles if she hadn't had a cooperative neighbor who was willing to split the costs on necessary shared work.

As far as the rules on whether you can convert two duplexes to a large home... I think you have to check with local rules and regulations.