I just feel this is like trying to apply logic to Santa Claus. The bug scene in Indiana Jones took place before the boulder scene or the dart scene (as TOD was a prequel), but in the "new" Disney ride adventure, they happen at the same time. It's a coherent story, but it includes elements from the movies that take place at two different times.
Hell, Indiana Jones isn't even Indiana Jones--dude doesn't even SOUND like Harrison Ford. Honestly, that takes me out of the Indy ride more than the time inconsistencies take me out of the Star Tours ride.
Here's a question: had Lucas just said, hey, we created a story that is based on scenes from different time periods within the story in order to immerse people in the movies with a "new" story (like Indy), would the time detractors be okay with it?