I put some time aside today to test out a recent snapshot with these changes (GregTech 6.14.15-62-g71bc561a), and it looks like blueprints are successfully Shift + Clickable into the Advanced Crafting Table’s blueprint slot now. 
The only other improvement related to this that I can think of at the moment is making it so you can Shift + Click a non-blank blueprint out of the Advanced Crafting Table’s blueprint slot into your inventory, like you can with the Autocrafter (not sure why it didn’t occur to me to mention that at the time I made the thread).