Have a work around for the governors that allows me to play 1.3 the way I would like.
GalCiv3GlobalDefs.xml, <PlanetGovernLockTech> changed to TranslatorTech allows the Govern Button to become usable when Universal Translator is discovered allowing access to the Auto Upgrade Improvements button before any other improvements discovered.
GovernorDefs.xml. Removing from the appropriate governors all improvements, bar one, allows the governors to be used effecting the sliders only and ensuring at least one building is built. (To remove all improvements from the governor prevents the governor buttons from showing up as does removing <AIOnly>false</AIOnly> from the governor.)
I am now able to have full control of what buildings get built and when they get upgraded from the start of a game. Whilst, tagging my colonies that are to be used for specialization and having the sliders governed for me.