KiCad net tie on inner layer
Sadly version 5 (and earlier) rely on a workaround for making net ties. This workaround as you noticed relies on footprint pads plus graphic elements on copper. Sadly there is no way to get such a pad to an inner layer.

Version 6 (planned to be released within a year or two from now) will most likely have a direct net tie tool that will not be limited this way.