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Sea stone is used in ID but we don't really know the circumstances of his scape. Overall I think the simplest assumption is that sea stone forces the captured to remain human so to speak so no weird bodies or abilities in any context. If I recall some people even felt weakened from touching sea stone.... A good number of paramecia would be impossible to contain with sea stone if the thing works the way you suggest which for plot reasons is inconvenient.
But that appears to be the case. In the Arlong Park arc we could see that Luffy's body could stretch underwater, and there is no reason to assume the seastone has a different effect than water.
So did we ever see a single panel where someone with a Devil Fruit was using their powers or had they body been altered in some way to prove that their bodies were still in their DF mutated bodies? AFAIK no.
Kairoseki is seemingly the condensed form of the sea water minerals in OP, so it will likely not need to coat a character over half to take effect, but on the other hand allows the prisoner to act like a normal human without going limp.
It's strange though, when he was in Impel Down, Mr.1 got injured by another inmate when he had the kairoseki handcuffs
So maybe it's a matter of different fruits.
Putting it that way the whole thing is really weird. If people with kairoseki cuffs don't stop being their element then there is no reason for them to be capable of holding people with certain abilities. If luffy remains rubber with kairoseki cuffs then there is no reason for him to be unable to remove them. There is no reason for them to have ever held ace for that matter. But then again it does seem like people remain in their element so to speak. Confusing....
Smoker also hit Luffy in the throat, right? I don't care if you're made of rubber, you still need to breathe.
If Luffys throat was squashed, he wouldn't be able to speak to begin with, because that's the place where we create "the sound".