At first I must say that since LivingEntity#setCollidable(boolean) is no longer in use SPIGOT-6399, it should be noted in documentation and marked as @Deprecated. 

It seems to me that the getCollidableExemptions() Set is also not taken into account anywhere else, because the code using it just doesn't work. If it's been dropped out, I believe it should also be noted in javadocs and also marked as @Deprecated.

Code that was used to test whether methods work: gist

It was said in comments to #6399 that one «..need to utilize scoreboard teams API instead.», but as far as I'm concerned, it would not allow disabling collisions for two players on one entity, while preserving inter-players collisions. If I am wrong, could you please explain how we could do so?