chakra is what keeps people alive. It's created by combining spiritual and physical energy of a person, if you run out of chakra you die, so it makes sense that a technique that was stated to give life to inorganic things can't give life to something already made up of chakra.
you do know that thats exactly how the bijuus came to be?,hago took the chakra of the juubi,split it from its body divided it into 9 places and gave each life,then gave each form as well.
So giving life to pure chakra isnt a fairy tail,nor is controlling the chakra of another person(that is what genjutsu does).
If muki tensei had such an inability to control things with chakra flowing through them,i think kabuto would say it. However he needs to touch the thing he wants to control iirc.
Susanoo isnt even some special ninjutsu,it is just chakra shaped into a warrior like construct that the user hides in and controls,it is no more alive than a rock golem.
In theory there is nothing stopping him,so far all ive seen are either refusal without explanation,saying he hasnt done it before,or saying he cant do it to chakra.