Very nice, copout!
When they set the bike up, they are supposed to move the tourpak back from it's "shipping mount"...if you take the liner out and look, there are holes which will move it back an inch or more...make sure they have done this as it will give your passenger a little more room back there.
With regards to the exhaust/intake mods...the dealer probably looked at you funny because from what I've been told, they have been instructed by the MOCO not to do any mods to them. It will be interesting to see if they will do any downloads to the ECM if you change things up...and we don't even know yet if downloads are available for the 110 w/mods. Of course, there will always be the other options, like PCM, etc, but you might have a hard time getting the dealer to touch anything that effects emissions.
As far as room in the tourpak...from reading here it probably has a bit less room, but it's a little taller with the hump....I'm sure you can get a King, but it you want matching paint, that's going to be a different matter entirely...if it can be done at all, it's going to cost big bucks, and frankly I would be surprised if it's even available as an option. From my understanding, they will not sell ANY CVO paint schemes to anyone other than a CVO owner, and to my knowledge a painted King, since it is not part of the original bike, might be impossible to acquire
The bike is beautiful, so log some miles...the power will make you forget all about some of those things you're not used to yet.