I agree with Zombie on this. It seems likely that the opening adventure is taking place to stop Soviet Agents from stealing something from that Army base. Then the story continues with the Mesoamerican stuff.

Remember the movies always have had a mini-adventure and the main one.

Raiders: The fertility idol in South America and then the Lost Ark
Temple of Doom: The ashes of that oriental guy in Club Obi-wan then the Shankara stones.
Last Crusade: The Cross of Coronado then the Holy Grail.

Why should this next movie be any different?