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In OmniFocus 1.1, you'll only be able to synchronize with one server at a time.

(You can switch between multiple server configurations and OmniFocus will ask if you want to replace your current data with the data from the server, and I sometimes use this to switch between my real data and some demo/test data. But as you point out, you lose out on some of the benefits of intermixed GTD if you partition your life that way.)