It's cool.
Further thoughts on Boney's place in the party:
[spoiler]In the interview with Itoi, he mentioned that when the game was still being designed for the N64, his forecast for the final battle was actually a lot darker and crueler. Pretty sure that means he was going to have the dog die at that point.
They didn't go that way, though. So what does Boney do? Well, he has heightened senses: he smells Hinawa and the boys, tracks down Duster, and finds the jar of pickles, among other things. He can fit in smaller places, like the hole in the speaker that the stink bug flees through. He's also part of the family, being one of the only two characters in the final party that's actually named at the very beginning: Flint's memories of his happy family include Boney, and when Lucas is in the field of sunflowers in Chapter 6, Boney is with him. This balances out the fact that he's a bit of a problem for the group since he's a dog: he's just as banned from Club Titiboo as Lucas is, and when Lucas works in the factory, Boney's stuck running a treadmill. Altogether, he's a mixed set of assets and liabilities, combined with a unique identity in the world of the game--which is to say, he's a complete character.[/spoiler]