It isn't a 'genre conflict for Star Trek' it is a conflict between the Star Trek genre element of the transporter with another agenda, which focuses on drama/narrative/plot. Since the transporter logically removes many constraints from a wide range of situations, it undermines the production of many forms of tension. I mean, one could also try to argue that this simply makes the task of challenging characters (in any of several ways, this can apply to gamist concerns as well) more INTERESTING. It is undoubtedly true though that it increases ones work, or else tends to beg for 'cheap answers' like "Oh, there's an ion storm, you can't do that now!" (which a LOT of actual Star Trek episodes did, though the nature of the excuses varied a bit).
The point is, if all I want to focus on is emulating the genre successfully, its not a problem, the transporter 'just works' and the players will likely use it to achieve their ends, and the GM will likely construct plots that read a lot like Star Trek episodes, and some of them will feature 'ion storms', but mostly because that's how the show worked (though it is likely that some dramatic tension is present in this type of play too, which it might enhance).