Maybe the other contractor is a friend, who knows? Obviously 10 yards of dirt and the labor is well worth 100 bucks. I'm not a fan of burying cheap corrugated downspout extensions. In our area it seems to have been all the rage in the late 90's, based on the number I've dug out and replaced with ridgid since you can't snake the corrugated. So IMO you're probably giving them a better value.
I'm not a LCO so I'm not sure how much my opinion counts but I don't think you're at all out of line. Maybe they'll call you back to topdress or regrade what sounds like a subpar job in a few years given your extra effort.