That was my experience with it, too. Microprose could do no wrong.
There would be a section on the gameplay itself and then usually some historical reference about the setting of the game. E.g. if it was a WW1 flight combat simulator, there would be a section on the history of aerial dogfighting and then specs on each plane.
I know that nowadays it's common knowledge that most people don't read the manuals and it's easier to get people into a game with a combination first level /introduction/tutorial. That being said, I feel like we lost something by taking out the manuals with all that rich historical detail.
It really added so much to the game. Many other games came with cool things in the box too, like Wing Commander with the blueprints of each fighter.
I guess part of the reason was that the games themselves weren't all that immersive. There were no cutscenes or long narrative. The tech simply wasn't there yet. The included box items made it more interesting and immersive.