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Correct, the app store does not recognize the already existing installation. There are several places this is being discussed presently. Apparently the only way to get the MAS updating feature is to purchase through the MAS. Some are reporting if the build is exactly the same the MAS may recognize the app as being installed, but that does not mean the auto update feature is available.

A workaround may be that vendors provide trusted existing license holders a coupon/rebate/apple credit so that the end users can re-download from MAS and require them to delete old installations/licenses. Although, that would be costly to the vendors. There should be a way to let MAS recognize the apps as-is; just like the iLife apps.