I wouldn't pay a markup on these cars... or any car for that matter.
I wouldn't say the price of the Golf R is asinine. It really depends on the position you are in, how much leverage you have, whether you pay a mark up or dealer adds, etc. The GTI Autobahn ends up being 45k after destination and factory adds (that's before the dealer gets ahold of the car). That's spitting distance from a Golf R. Gone are the days of paying 24k for a brand new GTI S with Clark Plaids. Cars have just become more expensive.
It seems that most dealerships are done with waiting lists and Rs are finally showing up to lots. In my area, they are selling for around 48-49k. That's only up from about 43k MSRP for the MK7.5 R from 5 years ago. Break that down further, and the actual factory MSRP for the MK8 is around 45k before destination and factory adds (floor mats, auto dimming rear view mirror, road side kit, etc.) stuff you can't delete.
I'm honestly surprised that this Jim Ellis place is willing to just show ADM on the website. Most places only have it on the Monroney under the dealer adds as showing it online will only deter prospective buyers.