I have read about your group's shattered star AP and while i have never neither played nor DMed for such a group, i imagine that your way might indeed solve the issue of the joke/minor encounters, even make them meaningful. But every character in this campaign was very murderhobo/militaristic/efficient etc. and it's not a group thing, we are capable of making other kind of characters but in this AP everyone went with the above approach, i think that the "treasure hunting" aspect of the adventure played a role here.
I think that you are talking about the infamous "XP problem", i solved that by leveling up the players at the points the AP said to level up.
About the combining encounters thing you mentioned, it's very rarely scripted this way (a lot of times it's scripted the opposite way) and quite a few times it can't be done becuase of the locales (super big dungeons, lots of space between the monsters). The one time i remember it scripted in this AP to happen (at Beyond the Doomsday Door) my players went all splinter cell on me.