They did that to a freed nine tails, Tobi released Kushina's seal before he did it. 1st Bee said the chakra Naruto took from Kurama was his forever when he was helping Naruto fight Kurama. 2nd Kurama's chakra is different from before, before it was full of hatred but now it's full of lifeforce (Yamato stated). Tobi was able to control a prefect Jinchuuriki but couldn't control Naruto or Bee and Kabuto never made Itachi use genjutsu (Tsukuyomi) on Naruto or Bee (broke out of regular genjutsu). Not all Uchihas can do the same thing.but at the same time its not just 3 tomoe sharingan (which tobi/madara used to control full fledged kurama) its the eternal mangyeko sharingan.. which i think can make quite a difference