As soon as Kakashi eye changes it was was to much for his chakra and body to handle and he passed out. So I think he doesnt even realize what has happend and even if he did he wouldnt be able to use it at his current power level. I dont think Kaskashi had control over his MS do to not being Uchiha until after the time skip. He still needed a loot of time to use it and get it ready as it was. I just think it took him a lot longer to lear how to use it. What do you all think?