Trek buys a lot more groupsets than any individual, same for Giant and all the rest, so they get better pricing. Buying it as part of a bike is usually more cost effective than buying it standalone.
Di2 is really nice. Modern mech groups are really nice, too.
Like most people who've used it for a while, I'd prefer not to go back. But I wouldn't spend a grand to add it to a bike that already has good shifting. (I'd rather have 105 and a power meter than Dura Ace Di2 and no PM.)