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Do we even know that his body is that way because of injuries though? While that is a possibility (and just as likely as any other explanation, since we know next to nothing about it), it's equally likely Tobi merely wanted an indestructible body. Given the way he favors techniques that leaves himself completely untouched and unharmed, wanting a body that can't be easily destroyed could very well be something he'd want.
Like I said, though, we know very little about it. And without knowing more about it, the state of his body really isn't conclusive evidence of anything.
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