While its fun to theorize we know little about the Rinnengans full abilites and even less on what Madara's MS abilites are & how he has lived so long and what he is capable of doing. Madara devleoped MS almost 100 years ago who knows what else he has developed in that time.
The fact of matter is Madara is in charge and the one giving orders to Pain.
Remeber this scene:
Madara: Hurry up and get the 9 tails bitch !
Pain: I'm god ....
Madara: You say something!?
Pain: No sir
Madara: Good now hurry up and dont F#ck up!
Konan: Pains never lost a fight!
Madara: Hoe did I ask you Shut your mouth ! Boy keep your woman in check and get me my sh^t !
Pain: Yessum !
I'm paraphrasing of course LOL