I have only played one Dye course and will be playing the one right next to it this summer, so my basis is pretty limited here. I don't think he ignored the natural layout on the one I played, he just manufactures something around it that is in some ways out of this world. I loved it because it was so unique. You have to go into a Dye course in my opinion with the mindset that you are about to play something very unique and just have fun with it.
I've played a handful of Dye courses in various parts of the US (several of them numerous times) and the only consistent theme for me is I've never had fun playing any of them.
The absolute most fun I've ever had playing golf has consistently been at The Homestead, The Old Course, in Hot Springs Virginia. I've played all three courses there many times (The Upper Cascades - Championship Course, The Lower Cascades, and The Old Course) and The Old Course has always consistently been the most enjoyable course anywhere for me. It was built in 1892 with updates by William S. Flynn and Rees Jones. It takes advantage of the natural mountain terrain and dynamics. At no point on any hole there have I ever thought "this hole would be better if." When I finished rounds there, I was surprised it was over and was left wishing there were more to play. Dye courses always seem to me like the round will never end soon enough and I'm glad to see it in the rear view mirror on my way out.