Having GFCC work like factories is probably for the best, but one thing I liked about the fixed construction rate of GFCC was that it more or less acted as if the training process of the actual soldiers was something that happens at a fixed rate and that can't be accelerated by additional complexes, which made sense. Someone isn't gonna become a soldier/tank driver faster by having multiple schools.
My dream scenario would be if the soldier training process was split off to a separate building that had a fixed training rate, maybe functioning similar to how academies continuously produce crew for space ships. GFCC would then in spirit only produce the equipment and vehicles and, once they've finished constructing a formation, they would draw their soldiers from your soldier pool, similar to how constructed ships draw from the crew pool.
Actually, maybe this function could just be added to the existing academy building. Right now academies have a setting that let's us change the quantity vs quality of the produced personell, maybe they should in addition have a setting that let's us choose how much space crew vs how much ground soldiers they produce.
(For the question of what should happen if you don't have enough soldiers in your pool and build a formation, maybe the easiest would be to have the formation stuck at 100% in the construction screen until enough soldiers had accumulated for it to be completed. Instead of having a conscript modifier like with space ships.)