The repetitive-contrastive stress in the sentence produces stress on "is", which can't receive stress when it's a clitic ("A clitic is a morpheme that has syntactic characteristics of a word, but shows evidence of being phonologically bound to another word" and "The term clitic is used in traditional grammar for a word or particle that cannot bear accent or stress....") bound to "where".
If your column isn't country data, where is it?
Here, the stress on the most-important word (for the sense of the question), is, contrasts that word and its sense with the second-most important word, isn't, in the contingency:
If your column isn't country data, where is it?
In addition, when the negated verb (isn't) is re-introduced as a positive verb (is) in the wh-question, that "repetition serves discourse informational ... purposes [and] contrasts or emphasizes the whole [wh-question] ...." ("Sentence Stress in Information Structure", Kent Lee, 2013, p. 8).
My observations about the prosodic stress patterns required by the intended meaning of the quoted question don't satisfy the OQ entirely. In order to satisfy the OQ, the reasons "it", "where's", or another word shouldn't or aren't likely to receive stress would need to be explained and, for good measure, an account of why such phonological observations would apply to written English at all should at least be referenced.
About the last, why phonological observations would apply: I'm either going to palm that explanation off as 'general reference' in accordance with long-standing evasive tactics at EL&U, or I'm going to misrepresent that explanation as being complete and entire in the rationale that written English, especially written English drawing on informal phonological features such as clitics, derives all of its informational structure from spoken English.
The other, the reasons another word than is doesn't receive the stress, are at least partly explained by the reasons I've given that is does receive the stress. Briefly and in summary, my reasoning is that the accurate interpretation of the question quoted in the OQ depends on that pattern of underlying stress. Beyond that positive explanation, the reasons another word than is doesn't receive the stress are best summed up as artifacts of there being no other good candidate than is for both the sentence and the phrasal stress.
Note
Successive edits of the OQ have put this answer somewhat out of step, yet I think it still might have some value as an answer to the original, unedited OQ.
- The title of the OQ was originally Why can't you say "Where's it?" not Why is "Where's it?" Grammatically incorrect? I responded to the original title, not the edited one. My response to the edited title, should I choose to make one, would summarily dismiss it: "Where's it?" is grammatically correct.
- The second edit ("Edit 2" in the OQ) implies, quite to the contrary of the poster's intent, that the OQ is a 'duplicate' (a 'duplicate', that is, in EL&U parlance, which parlance promotes a close similarity to duplication) of the suggested 'duplicate'. Accordingly, I have voted to close the question and removed any of my comments suggesting the OQ was not a 'duplicate'.