You exclude the fact that Madara is currently aware he's an edo.I suppose you haven't considered a few things...maybe that susanoo could only be accessed by the current version of himself. Also for all the all powerful many call him, it's only cuz he is an edo, think about it - how many times did he get hit where parts of his body were completely severed?? Had he been alive the fight would be decided ages ago. Remember he has rinnegan now which he DID NOT have before. This fight is on a totally different scale and honestly I am not sure that Harishirama (i think i spelt it wrong) would have a difficult time beating him or jus simply be unable to beat him (this version).
Perhaps he has his reasons for getting hit? Maybe to test the amplitude of the enemy attacks or because he knows partial regeneration takes very little time [so he just doesn't care for a severed limb]