Hi guys! I finally managed to complete all the expedition content after a week or so (I have to burn my vacation days anyways so I had some time to play) and I wanted to share my thoughts.
First of all, there is only one single instance where Spider enemies are a mandatory fight and if you're lucky you won't even have to fight them.
-In the Horticulture center, once you descend to the Warehouse floor do NOT enter the western room (spider nest). Instead, go south to the cryo chambers and fight the strongmen. Inside you will find 1 herbicide gas grenade that will be enough to clear the vines in the upper floor and progress with the quest.
-When accessing the Nexus of Technology. Do NOT go thrugh the spider caves. Instead dock your ship in J6, then move 2 squares east through the marsh to L6 and in the eastern most section there is a dynamite wall that can be broken which will act as a shortcut to L7, the entrance to the NOT.
-In the Nexus, there is one unavoidable spider fight in security, lvl 7 (or 6, I don't remember). If you have the security keycard from the higher levels you can open the eastern and western doors to the spiders. This will trigger the strongmen to activate and they will kill ost of the insects. The biggest lair is to the south but I just mashed the space bar until combat ended. I felt sad that I had to put the handmaiden down but c'est la vie.
-In the JSHQ it depends on your build. Once I was naked, I stealthed until I found the Haxorr and then picked the lock on the door where my equipment was stored. I didn't have to go east to the spider lair for TNT. I guess I lucked there.
-To get to the Northern manufacturing facility, where the sub is located I parked the boat in Geyser Village and genocided the natives. Then went east and only fought the crabs and strongmen (individually, because I'm fucking stupid).
-Finally, I NOPED out of the LEMCO facilities, just sailed along the edge to L2 where the sub was parked.
-It also goes without saying that you should never go into any vent since it's a coinflips chance there will be spiders inside.
As for the Quarry and the Citadel of Life I have no idea. I sided with the Expedition instead of the Pirates so I had no reason to go there.
I also want to say that the sub section freaked me more than it should but I fucking loved the Abyssal station fights. When the shit hits the fan it's absolutely wonderful. For some reason when the spawn started falling out of the holes in reality I wasted too much ammo trying to fight them (I just could not hit them) until I started chucking incendiary grenades. Suddenly I could hurt them and my monkey brain went, "shadow creatures are damaged by light!" - so I died when I tried throwing flares at them.
The second time I though that the gates were there to stop the endless spawn so I rushed back criss-cross, locking the gates behind me. I was legit tense during the whole fight because I thought the station would collapse on me.
I accidentlly overlevelled on shadowspawn because I forgot the way back once I had the Torch. I kept shooting at the shadowspawn while trying to figure out where the hell the gate switches were located.
Finally, I gave the ACORN to the Occulus since the Protectorate is a no-no, Aran is a weeb, the doctor wouldn't know his asshole from a hole on the ground and I don't even know what SGS would use it for. I kept the Torch because it's mine and worth far more than the 6K charons Aziz would give me for it.