Michael, in the 5D Field Report you state that: "The 5D's full-size prism doesn't leave room for [a pop-up flash], and so the Canon 1 Series, and now 5D camera, don't feature pop-up flash. It's as simple as that."
While this may make sense comparing the camera to APS-type DSLR's it doesn't make sense when comparing to film cameras, which are - by "nature" - all full-frame. I have a Minolta Dynax 7, which has a 92-94% 0.8x viewfinder (compared to the 5D's 96% 0.71x VF) AND an on-board pop-up flash. The "full-frame" prism doesn't prevent it here. Also look at the Minolta Dynax 9, which has a heavy duty weather-sealed pro body, a 100% 0.73x viewfinder, and an on-board flash. No problems there, despite being a "full-frame" 35mm film SLR.
And looking at the design of the 5D, I see no reason why there shouldn't be room for pop-up flash. The part of the flash that takes the most space (the flash itself) is usually placed in front of the prism, where the 5D seems to have room (it lacks the "nose" of many other (D)SLR's).
IMHO, it's not a question of wether there's room or not. It seems to me like Canon have made a decision that a pop-up flash does not belong in a pro body, despite the obvious reasons for it's usefulness. Just like their decision that the mirror lock-up feature must be buried deep into the menus despite the loads of complaints from its users.