Today the official NAV team has published in their official blog the new Cumulative Update 9 for NAV2013R2.
In this CU9 we can find new cmdlets for Powershell and speed up the merge between versions or products. These utilities are prepared for different versions and not just NAV2013R2 but it is not compatible with dataports, forms oR section-based reports.
In this link you can find a PDF file explaining how to use these new utilities.
In this link you can find the Powershell files and some demonstration objects in order to start creating the initial tests.
The following chart shows the percentatge of success when the automatic merging is working on the demonstration objects Microsoft provides. Also the percentatge of conflicts that are yet to be reviewed.
With this information available I have created a new merging utility you can download and use completely for free. You can find it here.