I only see two kinds of major philosophical disagreement the Libertarian Party should tolerate in its official positions.
One is on franchise issues, the big three of which are abortion, immigration, and intervention. Libertarianism's core value of minimizing aggression against enfranchised individuals will never dictate unanimity over how attributes like fetal development or citizenship affect enfranchisement.
The other is about how far to stay on the LP Freedom Train as it heads toward the anarchocapitalist cliff that we minarchists are confident America will never choose to reach. We all want to get the Freedom Train moving, but it won't ever budge if we wait until we all agree we'll get off at the same stop.