They could probably get away with it, they just need to take into account when you need each Pokemon and adjust the design and distribution accordingly. For instance, let's say you go through the left half of the hexagon earlier in Black 2, and as a result you fight Skyla earlier as well. Since Chargestone Cave has plenty of Pokemon that you can use against Skyla, it's right where it needs to be. Sure, Black 2 gets many of those Pokemon earlier, but it also needs many of those Pokemon earlier, and as long as the Pokemon in it are available at a reasonable point in the game. The problem with changing the storyline path is that the Pokemon placement is designed with the original path in mind, the Pokemon distribution has to be altered to accommodate the new path and make sure the locations are still reasonable, and that you have enough options to suit the storyline's need (particular in regards to upcoming gym leader battles). And with version exclusive paths, you need to make sure the distribution is reasonable for both paths. This would require careful design and planning, we've already seen what can go wrong if they mess it up.