I think fixing the roll-off points would go a long way to improving the behaviour of naval facs, i remember once playing around with rally points for ages trying to get the ships to leave cleanly when they finish building.
In-game, I don't see players build a block of naval yards like in the linked images, it is usually a dragged line and then maybe another dragged in front a few squares away which poses few issues for the frigates built, grids are reserved for air only.
Having different faction placement potential is not going to work - you will get players always picking a specific faction for different spots on Setons for example.
About the AI - is it possible to have the larger-skirt version blueprint available in-game for just the AI to build ?