When some have water cooling and some don't and they're going down the line one after the other, while it shouldn't happen, it's not a huge surprise that it slips by Harley's assembly line. This is the same line that we've seen build mismatched color parts on some of the CVO bikes several times. If they can miss an error in something as large and obvious as a fender or painted lowers grabbing the wrong filler panel from the pile as the bikes roll by is within the (facete mode=on) margin of error.
Possible explanation, since the lowers are so similar, but on the other hand, all the 103's and 110's require a gasket under the trap door on the transmission case and mine was missing as were a couple more bikes on the showroom floor.

But ..... Wouldn't the prototype parts have been made with production-intent processes? I just can't believe stuff like this couldn't have been avoided. 
Prototype parts are often custom machined parts that later get replaced by injection molded or die-cast parts for production. Some of the lightening and webbing required for proper material flow on cast parts, along with the possibility of porosity, introduce weaker cross sections therefore an inherently different part altogether from the prototype. This combined with an assembly process that apparently lacks oversight by a competent quality control system allows so many problems to be passed along to the consumer.
Regarding the missing coolant, is it possible that it could be cooking off and/or entering the exhaust stream? Only other thing I can think of is a pin-hole leak that, when under pressure, streams out onto a hot surface and evaporates away without leaving a tell-tale puddle. Best way to find that would be a pressure test on a cold engine with the thermostat open.
