Bay addresses this in the audio commentary for RotF. Real-world geography simply has to take a back seat when it comes to telling an evocative and exciting story with multiple recognisable locations, referring to those who get hung up about that sort of thing as "geography buffs".
Bay: Most people have never been to this brand new Smithsonian museum which exists in Washington, which is at Dulles airport. Now, I
wanted to shoot in this airforce base in Tucson, which is a
gigantic... it's not a wrecking yard, but it's a yard where they
reclaim every single plane that's ever been flown in the air force and
they use them for parts. There's actually a section of this
gigantic... and I'm talking it's miles of desert, and they line up
these planes in a very organised fashion, and actually the Russians to
this day keep it still on satellite every day because they want to
know if we're moving or parting out any of our B-52 bombers which are
still, we have a bunch of bombers there and if we need spare part for
our B-52 bombers, which are the ones that carry the nuclear weapons.
It sounds very cold-war era, but this is where every single plane in
the air force, unless it's crashed, goes to this yard.
For the geography buffs, I didn't pull it off, but for most people, in Taiwan, don't know where this museum and this Arizona airfield
exist and so this my way of jumping time, well, not jumping time but
jumping locations by showing the desert outside this museum
Note that if the filming locations (Giza and Luxor, for example) were 'real-world' accurate, the locations depicted in the film would be hundreds of miles apart and would take entire days of travel to get to.