Applying overlay changes ownership of root partition

I recently needed to add an overlay to my build. I do prepare the overlay as normal user. Unfortunately applying the overlay does change ownership of the root partition, as the overlay is applied using rsync. As a quick fix I change ownership of the overlay folder before applying it. In the long run I’d appreciate if there was a solution that could just apply an overlay without messing with files and folders that are already there…

Any suggestions are very welcome!

I was reading up about the --inplace option of rsync which might be a possible solution. What do you think?