I sort of think the whole thing is by design. The Pub establishment is well aware that perhaps a majority of their primary voters want candidates that tend to be politically toxic in general elections. So the dice are loaded.
As Cohn notes, it's not just that the dice are loaded towards the more moderate candidates in the presidential primaries, but that things are skewed the opposite way, towards more conservative candidates, when it comes to GOP Congressional representation. (As he points out, 40% of all GOP primary voters live in the 18 most solidly Democratic states. Yet those same states include just 7% of all Republican US Senators.) This skews people's perceptions of what the median GOP primary voter looks like.