I can't remember if the pillars have an effect on the saucers, all I remember is that this part of the mission is short. I first retreated into the hallway for a better defensive position for the first couple rounds, I didn't like staying in the big room at first because the saucers can flank you too easily and you take needless damage, though I'm sure it's possible to beat the mission without retreating. Once I got the first wave, I reentered the big room and took positions behind the covered areas.
And don't worry about the second phase of the mission because in the 2nd part there are plenty of boxes with ammo etc for you to resupply.
I didn't know the final mission was the final one so I brought only minimal equipment along and when I suddenly realized I'm in the boss fight in the 2nd phase, I already thought damn maybe reloading from the base is necessary but it turned out to be a lot less troublesome than I thought. I went full aggro on the 2nd part of th the final mission, lost two of my crew (Schaffer and Josh) because I went Omaha Beach on the enemy but it was fun and all my "last mission paranoia" about running out of ammo turned out to be unnecessary. No need to hold back with anything, all my non-snipers took turns in picking up grenades from crates, handing them to other team members who were closer to the enemy and chucking everything about. Didn't use any special skills except for Morten's aimed shot and Sam'd headshot. Jenna did the best in the end, Josh was useless to me as I didn't stimpack him into anything useful, earlier on I used him to take down shields but I hate the cooldown time for this skill and in the the last mission I didn't diddle around and wait so all I let him do was run to crates and hand stuff to other team members and draw some fire. He did, and died for the greater cause. Schaffer died because as awesome as his shield is, his health isn't so once the shield is gone and he stays in the open and gets hit by two shots, he'd dead. Thirteen was the absolute badass in the last mission, he took so much damage and everyone kept sending him medikits, I let him stand out in the open a lot because if you let him take cover, the enemy will start shooting at my offensive characters and I didn't want that. I'm sure one can tackle the last part in a more cautious manner but I enjoyed rushing and going on the offense as quickly as possible.
My overall strategy was to turn Morten, Sam, Jenna and Gina into dedicated snipers and let them handle all the ranged combat. All 4 had aim of 10 or more.
Aim of 8 was good enough for long shots in the campaign earlier on but in the tough missions I only let people with aim of 10 or more shoot beyond medium distance, all else is a waste of action points and ammo.
Thirteen, Linda and Schaffer were my meat shields/bullet sponges. In the first phase of the final mission they get opportunities to dish out some close range damage but in the second phase I didn't have them fire a single shot, distances are too big.
Thirteen can absorb a massive amount of damage with the Tank Prototype armor, I stimpacked him enough so that he can still have acceptable agility plus if he gets behind too much you can use his teleport. Linda can obviously self heal but that skill isn't very useful in the last mission where it's go go go, I used her mostly as a medic.
Schaffer with a Scout VI is surprisingly tough, that plus his agility makes him an ideal runner. I didn't waste aim packs on him as I used him for drawing fire, throwing grenades and retrieving crates.
PS: I love this game, was very pleasantly surprised