What they actually mean is rather “these two things are very dissimilar”, or “these two things are unequal”.

I think what they mean is “This is an invalid comparison”. For instance, the idea that two concepts are “apples and oranges” invokes the idea that apples and orange can’t be compared. But of course they could be compared as fruits (which would you prefer to get in line at the cafeteria? Aren’t you inherently inviting a comparison? I’m with you on that).

However, if one were asking whether golden delicious apples are better than honeycrisp apples and someone butts in that navel oranges are the best, they’d get the same “navel oranges and golden delicious/honeycrisp apples can’t be compared” response because they’ve brought up an invalid comparison in the context of the comparison. Apples and oranges.