Oh yes, and Wolfenstein actually ran quite well even on a 286. Higher res and framerate than same time period Amiga titles. Aside from the additional inefficiency you mentioned, I think 3D is an area where none of the Amiga's specialised hardware chipsets helped (or at least, nowhere near enough / as much as they did with 2D), and the CPU performance disparity started to really show.
Amiga stopped investing/improving their unique hardware chipset and PC's simply overcame that deficiency by sheer CPU power and improved graphics output standards (EGA->VGA).
