But won't this just mean that two candidates from the same party will end up on the General Election ballot?

This outcome will likely happen only in jurisdictions where one major party has a dominant registration advantage. In those districts today, the election is basically over in the primary, before a significant number of voters have even had a say. In many districts, our current election system effectively shuts out an actual majority of voters. This shutout allows special interests to force extreme agendas through threats of primary election challenges in party strongholds.