Thats pretty much where i landed a few years ago. So much time was spent trying to figure out/work around system builder that i gave up. I build the GUI in vtpro and add all the join numbers. Then i copy paste the pages into the system builder generated vtp files. I use global presets for simple activity/off macros.

System Builder has been great for 1 room systems and simple distributed AV. Once the requested feature set grows beyond that a programmer is used and i go back to wiring the racks.