Has your frame shipped yet? If not, call Peter (I'm assuming you're getting this from him based on the CS- designation) and order the Neco headset. Did he not offet it with the frame?
What are the "glaring' issues with the headtube length and chainstay length? Can you not get your bars low enough?
I bought this frame "new" second hand. Owner had a replacement frame coming in and sold it to me. I ended up taking everyone's advice here and I ordered a neco on ebay. It's cheap enough where if it works, great, I saved a few bucks. If it doesn't then lesson learned.
Regarding the geometry issue with the head tube.... yes it is indeed just all about handlebar height. The XL of this frame locks you into a rather large stack height number. I can some what work around this and can run a negative rise stem if I have to. This frame was very touch and go for me because it's a tick or three off my ideal bike fit numbers.
The chainstay length issue is just that, the chainstays are about .25" to .3" bigger then they really need to be for this size bike. This all boils down to this being a design that supports front derailleurs. If you ask me, they should have foregone that option and reduced the chainstay length to hit the new generation of drive train and bike geometry standards.