Some crossovers, like a Doctor Who/Stargate crossover, makes sense. Other crossovers, like a Fallout/MLP crossover, makes a significantly smaller amount of sense.
I suppose if they had fun writing it and some people enjoyed reading it, what's the real harm? At least they're not the ones mucking up actual lore and gameplay.
You know what a better crossover would be? Rocky and TMNT. Then rockys turltes, cuff and link, could get the ooze and they would be trained by rocky to be boxing turtles.