Well, I think "rules first" design is great, so...
But as far as in-game representation? It's the fighter getting in the targets' face, keeping their attention, maneuvering them away from his allies (within the area the minis occupy), etc. Marks get overridden because keeping someone's attention and focus is rather exclusive. I guess a more "realistic" rule could be that if the first marker doesn't choose to give up their mark (as a free/no action), then neither mark is effective.
Ultimately, I think marking is no more "rules first" and game-y than HP or AC.
I disagree that it's "half-baked". I think they did focus on rules first, but made sure it made sense in-world as well. I think the ideal is a feedback loop between rules and in-world representation, where each informs and suggest alterations to the other, until they mesh. I think the most important thing is good rules mechanics. But there are lots of possible good rules mechanics, so an RPG designer should choose ones that make for a sensible story.
I think "rules first" works quite well, in many RPGs. The vast majority of indie RPGs are "rules first", in my experience.