So ive recieved the 'Ultimate' box set and the IMAX sequences on disc 6 are the same colour grading as the blu ray.
On some of the later TV spots for TDK, the colour grading is more in tune with the BLU as well. Maybe besides the other problems with the transfer, the colour grading is infact correct on the BLU? I certainly prefer the advertising materials look, but it might not be the final finished grade approved by Mr Nolan.
From my understanding, promotional material is sent out for use most of the time while the film is still in production. These clips from a Assemble edit will be raw and proberbly have a blanket colour grade or one done by the marketing team.
After picture lock, the final grading will begin. If the deadline is tight, it is common that the film can be completed very close to release. (this was the case with the movie 'The Rock' with theatrical prints still being 'wet' from print when arriving at cinemas).
The 35mm stills in the OP are interesting. Is there a 'bootleg' CAM from back in the day floating around that would have been a capture of a 35mm showing?
I don't condone such things, but outside of a 35mm showing somewhere, it maybe our only way of getting to the bottom of it.