The good news is that is a state of the art system for building showers. So we know you are dealing with someone who knows how to build a shower. That Kerdi stuff is suitable for a steam shower and will keep the moisture AND water inside the shower where it belongs.
I can't tell you how many nightmare stories I've seen or read about regarding poorly constructed showers that leak and turn moldy because the installer had no idea how to build a leak-proof shower. Apparently there are still people out there who think tile and grout are meant to stop water from migrating to your floor and walls.
I always say I would never but a home with a walk in shower unless I saw it built. I had a client almost buy a condo with three walk-in showers. They moved in and didn't close due to financial troubles with the builder - by the time they moved out six months later, every shower was leaking. I used to think tubs with showers were kind of dummy-proof but I just replaced a tub for a friend in a ten year old condo. The tub (and drywall below) had been "repaired" over and over since the condo was purchased.
When I heard $1000 dollars for material, I thought that was really steep for some dry pack mortar (4 bucks a bag) and a $60 dollar pan liner. But I know that Kerdi stuff is expensive. And that is a good sized shower.
Not sure what to tell you regarding his oops/price. I'm of two minds on the subject. I've been on both sides of the equation and can understand mistakes and mis communications happen. I also know there are unscrupulous contractors that like to play games.
I suppose you could always bring in another contractor to give you a price for a similar build. That could get messy. Especially if you can't find another Kerdi guy.
You could also post over at the John Bridge tile forums. There are a bunch of pros over there who do Kerdi. In fact, it's their favorite system. They are a REALLY friendly bunch over there.