After 1 year, do we have a solution?
I ended up posting a similar question here and in StackOverflow.
If you tier some solution even if unofficial I believe it will help many.
After some analysis I see that a good part (package name, application id, application name, etc.) of this problem can be solved with the possibility of creating config.xml, for flavors, that could be selected via parameters of build, run, etc, example: $ ionic run android --flavors=free, and config.xml could merge with base config.xml.