There is a difference, most films are composed for a particular ratio; whereas TDK and TDKR were both shot with a 2.35/39:1 crop for general theatrical exhibition in mind.
Providing a scope ratio is appropriate though limited in its appeal, because the filmmaker intended there to be a scope version to be made. Since an IMAX frame has more height latitude the optimal pertinent visual information to be extracted for the 2.39:1 ratio may not necessarily lie in middle of the frame.
There in is the problem for CH setups, they can not simply crop or mask out the IMAX scenes because they will miss the optimal framing for that ratio.
Though what you are deriding by comparing it to P&S of old is not wholly accurate or relevant to this particular release due the fact the director kept that ratio in mind.
Now the opposite happened with MI4, the IMAX scenes were left cropped for scope on the BR. Personally I would have preferred a changing ratio but the director decided not to do that.
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