I get that Fridge Logic / Plot Hole Critiquing / Whatever can come across as really inconsistent and hypocritical at times, but the way I see it, is that each movie has a set of scales. If a film does enough little things right (and at the right times. ebb and flow, rhythm and structure and all that) it can weigh down the scale one way, so that when something ridiculous comes along, it doesn't tip the scale back into "Noooope! I'm OUT."
If Karl had hunted McClane down by following his bloody footprints as soon as that flashbang cleared, bad guys win, end of movie. But Die Hard does almost everything else perfectly, so I don't care.
The ending of Edge of Tomorrow probably has serious issues, but I haven't questioned it yet, 'cause I walked out of the cinema with a smile on my face.
And you're right. People direct a lot of criticisms at Crystal Skull that can be aimed at other films (the raft in Temple of Doom is pretty much the same thing as the fridge, I agree). But! Crystal Skull is almost entirely devoid of all those little moments in the other movies that buy goodwill.
As for Dark Knight Rises, I never really heard people state that the plot holes were why they didn't like it. The other movies had plot holes too. I think the film (for me, anyway) just didn't buy enough goodwill (or would buy goodwill and then lose it) because thematically, it felt inconsistent and not clear about what it was saying.