"If ever there was a tool that didnt need a gui its rsync. Idea is to keep two folder structures in sync"

rsync is a tool to copy data - it can keep two folder structures in sync but that is not its sole purpose.

Unison https://www.cis.upenn.edu/~bcpierce/unison/ is a tool to keep two folder structures in sync - that is its main goal but it can have other uses.

Unison happens to have a WIMP style GUI.

rsync could have a WIMP GUI and a console one. One does not preclude the other. I think you are right that embedding rsync in a more narrowly focused app might be the best option but it is not the only way.