I think the most simple solution would be if B4A would support Manifest templates that are stored in the Project folder and will be only used for this project. So if your app needs modification of the Manifest you can edit a local copy of the template.
With this method you don't have to check the "Don't overwrite Manifest file" option and so you don't have to always manually edit the Manifest if you just change version number of your app etc.
@Erel:
How about this solution? Should be easy to implement and I think easy to use. Just search for Manifest Template in project folder. If not exists search in B4A program folder.