From the reading of this adventure, I feel that some Seven Samurai inspiration was involved as well

I don't think there is one right or wrong way to run this encounter. It all depends on the style of the GM (I did a Dawn of Defiance campaign and there is a swoop gang led by some gal named Kessra, i changed her and her minions to use shock whips to knock down heroes and also drag them around the map, my players had a hoot over that). Myself, I'd be ok tracking both swoop and rider HP, but I also confess that my memory combined with the cheat sheets I use make that easier for me than it might be for other people.
Also, I'm somewhat confused. Did this encounter already happen, or is will it happen soon?
I would say that treating a character on a mount/speeder as a single entity is fine. I might give the swoop riders the
Mounted Defense feat and then allow the swoop's DR to apply to the rider, since I'm not using the swoop HP or Ref Defense. Or give the swoop riders a different bonus feat to simulate their swoop (such as Toughness for extra HP, or Running Attack to simulate shooting on the move).
I don't personally see anything wrong with the heroes using Autofire to hit swoop riders, as players often come up with imaginative ways to defeat their foes. You might require them to keep track of their Autofire attacks so they at least have to swap out power packs (though that may be a detail that others don't want to deal with).
I don't have many ideas for mini encounters, but if you follow the '3 types of opponent' rule I read about once, that can make an encounter more interesting. The first wave, you have foot soldiers and swoops mentioned. Maybe throw in a couple battle droids or attack dogs that behave differently than the other combatants. If I'm fighting 4 stormtroopers with rifles, an officer with a pistol, and a probe droid with a blaster cannon, I need to make some tactical decisions as my first action. Do I shoot the officer before he inspires the troopers? I can only hit any 2 troopers with a grenade, but it would drop two enemies out of the fight. Maybe I need to hit the droid with a missile to eliminate the biggest threat. Making combat into a interesting puzzle to solve can help with encounter building.
There is a Pathfinder adventure called Defenders of Nesting Swallow that has a similar premise of defense with waves of bandits attacking a village. One of the main points made in the adventure is strengthening Village Defense by training villagers, flooding a field, building barricades, etc. The adventure uses the threshold of 10/13/16/19/etc Defense Points to say, "ok, at 10 Defense Points, some archer got a lucky hit on a bandit and he goes down before the encounter starts, at 13 points another one got bogged down in the sunken field after his horse falls and he decides to escape rather than fight." This simulates the villagers helping, but without the need to have the GM's eyes on HP or Defenses. That allows you to focus on the heroes.