Yes dyndolod/texgen should be run after PG. It used to matter less before PG generated a plugin and the diff file.
As for the JSON issue. There is a bug that the JSON has `null` as its contents only if PG patched zero meshes. So that's likely what you are running into. So if you are running into this issue and you're expecting PG to do something, it isn't. So likely a misconfiguration in the PG GUI.
I made an issue here to fix the JSON issue for the case where PG patches nothing. https://github.com/hakasapl/ParallaxGen/issues/171