That's a very special kind of question: one that's almost entirely about definitions of words.
On one level, yes, this is just a definition issue.
On a deeper level no, because particular answers to such questions place the phenomena into a specific framework. Notice that two answers to "is helium a molecule" arose not because two people consulted two different dictionaries. They arose because these two people are used to thinking about molecules in very different ways -- both valid in their respective domains.
In that sense this "special kind of question" could be about defining terms, but it also could be about the context within which examine the issue.
I agree that the disagreement about whether a helium atom should be considered a molecule is related to what mental framework one slots the question into. I don't think this in any way stops it being a disagreement about definitions of words. (In particular, for the avoidance of doubt, I am not taking "X is a disagreement about definitions" to imply "X is trivial" or anything of the kind.)
The physicist and chemist in Kuhn's story could -- I don't know whether they would if actually asked -- both have said something like this: "It t...
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