I disagree. The primaries and associated rules are designed by the state chapter parties to pick their candidates. The winner take all model may push a popular candidate out of contention resulting in a third party run.
When has that happened? What I see are independents gaining votes in a number of states. Enough to give them a toehold in the general elections. But the winner-take all policies give their votes to the majority vote holder, giving them nothing.
Ron Paul and Allen Keyes are two recent examples. What type of election are you talking about? Independents parties don't usually have Presidential primaries because they are small enough to caucus to determine a cadidate. And winner take all primaries are not held everywhere. Some state parties distribute votes, but that still has no bearing on what independents do.