So you're saying that different parts of Susano'o have different chakra quantities in them, making them stronger/weaker than one another? If yes, then it would make sense, but still, a weapon has to be just as strong as the armor, since the weapon is taking the damage impact every time it hits its target, just like when you hit something with your hand - both you and that something take the same damage.
I hope you aren't implying what I think you are implying...and no, a weapon doesn't need to be as strong as the armor. The weapon being strong enough to strike something=/=weapon being as strong as the armor. Not even seeing how you are making this correlation. That only means that the force that is applied on the weapon every time it hits something is weaker than what would be needed to break the sword. Has nothing to do with the armor.
Don't compare Tsunade to Kabuto. Prime Tsunade admitted inferiority to P1 Kabuto in terms of Chakra Scalpels' strength. The same Kabuto
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Obviously Kabuto got much more proficient with using them, since we all saw what he did to Itachi.
Where did she say that? Cause I only remember her saying that he's more talented. Even if that is what he said, there is still absolutely no proof from your side that he'd jump from a level where he cuts Susanoo swords, to cutting the actual Susanoo itself.
So it's not surprising Tsunade went for kicks and punches against Madara, since they are much easier to execute, while she resorted to Chakra Scalpel only during the moment she was standing still pierced by Susano'o.
Except her attacking Susanoo requires no excessive movement bar the movement it takes for her to get the position where she needs to strike it, unlike when she was in her Taijutsu fight like Kabuto, where they were both moving throughout the whole fight.
Of course it deals damage but Tsunade wouldnt use a punch if she was trying to cut something. A chakra scalpel wouldnt have been effective enough compared to her Kick/Punch in wanting to destroy all of the susano.
I dont think we see how she broke the two susano swords, she removes two of them from her abdomen with her bare hands.
If it were strong enough, it would have gotten past, and cut Madara, and damaging him heavily enough puts him in a dead state, which lets them seal him. Not to mention it'd create an actual opening where the others can strike, instead of just a crack.
You're right about the last part though.