RK is a syntactic representation. Even though the words in 'run up' cohere semantically, they are separate units when it comes to diagraming. There is not a watertight one-to-one relationship between them. 'up' is an adverbial particle that is tagged onto the verb in the same way as 'in' is onto 'come' in 'May I come in?'.
In other words, 'come in' is a free combination of verb plus particle, while 'run up' is a phrasal verb. I agree wholeheartedly, but the point you are making is beside the point I was making, which is that when I diagram these combinations, I regard them equal in that they both comprise a verb plus an adverbial particle.
run ≠ run up --> up = modifier
come ≠ come in --> in = modifier :up:
Probably the etymology of those verb phrases could shed light on the issue -- i.e. where did they come from? The American text House and Harmon is pretty good at considering etymology. The OED could probably help too.
But that's more research than I am willing to do. In a CSD (competitive sentence diagramming) situation, as judge, I would accept either version.