In my mind, changing parts on a new bike is normal. Who doesn't replace the saddle and pedals? Why would you want the bike to come with factory fenders when the mfg. does not know the width of tire you are using? Tires...I had them switch those out before it left the front door of the LBS. Racks...I'll choose my own along with the bottle cages. Stems...if you didn't change that out, maybe your bike doesn't fit you as well as it should (or the shop was too lazy to fit you properly).

I'm real sure fulltime tourists spend much more time riding than most; they have a reason to be pretty picky about things. Some of those things may not be so obvious until the bike has been ridden X amount of miles.

I'm newish to bicycle touring; this is just the way I look at it. Bikes evolve. Change is good...sometimes.