I've never liked how vague the difference was between Paramecia and Logia.
Is the difference that the Logia user can control the "element" in question, like the way that Smoker controls smoke?
Well, Mr. 3 wasn't a Logia, but he seemed to control wax that was outside of his body.
Is the difference that the Logia user's body BECOMES the element? If so, there are paramecia fruits that act in the same way (luffy's of course, but mr 1's, mr 5's, and some others). These fruits probably differentiate two classes of paramecia; ones which alter the body material entirely (those mentioned) and ones that allow some power (valentine, golden week, robin, buggy, alvida, etc)
So the only difference I can see really is degree. Luffy or Mr 1 can't melt themselves to put themselves back together, although any of the Logia users were able to. This makes it hard to describe the fruits in a way that gets this across without making them sound the same.
About the seastone cuffs thing, I would think that they would simply nullify the effects of the fruit (except the curse) entirely. There's no need to apply any "logic" to this; that'd just be "how they work" (much like you can't apply logic to denden mushi or lots of other things; they just exist because oda thought them up). If luffy's body was still rubber, or Crocodile's still sand, for instance, the cuffs would be pretty useless against them.