Yes, you can use a pre-install script in the package with an uninstall <bundle id> to remove any pre-existing versions. Note that this process will wipe out any app cache as it is a completely uninstall so that may have undesired results depending on the nature of the app that you're updating.

 

To otherwise cleanly upgrade to a new version of an app you need to use an app that has been compiled under the same bundle id, with, with an incremented compiled version, and compiled with the same signing signature as the original app. You then need to modify the existing Package containing that APK with the new APK version and increment the Package accordingly.