---Although perhaps the digital intermediate process is also at fault here. No longer actually physically editing the film on a kem or movieola and on a digital avid machine. ---

Speaking as a professional (student) editor, the editing technique (using a kem vs AVID) has nothing to do with it. Until color-tweaking via DI (dig. intermediate) was widespread, most movies were conformed (negative physically cut to match, or "conform," to the workprint, in these cases an "edit decision list" or EDL that editing programs like AVID generate) after the editing process is finished. Today, that's "online editing" - making the 4k fully-color graded and everything edit to match the edit done at SD resolution by the real editor. But non-effects heavy movies still conform (there really isn't a cost advantage either way here).

Although I find it interesting that you note Crystal Skull's "DI" process. That's not how it was done. The movie was shot and cut on film, which means it was color-timed through the duplicating process like old films. They just used modern color grading styles because that's all anyone knows how to do anymore.