I don't believe a lot of people know about it so I decided to try both on a Double Double (I also went with no tomato). There's no added charge for either option
The default at In-N-Out when you get grilled onions is that they're diced, while the default for fresh onions is more-or-less a whole slice of onion. But you can also request for a whole grilled onion slice (or more if you like) as well as getting the fresh onions diced.
I think grilled or fresh, I prefer the onion at In-N-Out diced.