To concur with aaron's comments. I went on the Porsche factory tour when they were assembling the Mk2 GT3's engine at the Stuttgart factory and they describe how much more labour intensive it is to produce the factory "specials". There was a separate section requiring dedicated "meisters" who would hand assemble, balance etc those engines that could not be done in the conventional production line.

In no way am I suggesting that Honda affords a similar proportion of their production budget in assembling Type R, but I would not be surprised at all if the costs to produce these cars are a LOT more than a standard Civic due to not being able to exploit economies of scale as a result of the customisation and specialist labour required to create the hardware that goes in to these cars. In that respect, paying $10-$15K more than a mainstream item is not an unreasonable ask. If anything, I suspect these cars make less profit for Honda as a product but is compensated for in the branding and awareness exposure.