Hmmmmmmm.
Eyeballing the 2.4 trunk, I notice that the Bolter has a 'throughwall' flag of 2 (which, judging from quick grep + skim, means that it should be able to penetrate up to two walls of thickness less than 8... units of some sort, at reduced damage (the first penetration divides damage by sqrt(2), I think; the second, again by sqrt(3)). For comparison, all human laser weapons lack a throughwall value, the sniper rifle = 1, the coilgun = 3, and the chain gun has throughwall = 5.
As a side note, weapon preferences might change if the display showed estimates of post-armor damage (after, say, you've already researched the armor).
e.g. (all numbers from 2.4-trunk)
laser rifle: using pulsed fire, 3 shots, laser-medium damage type, "42 5" damage value. 12 TUs cost.
If I read the code right, each shot can do 37-47 points before armor... but then, we subtract damage reduction from armor. Alien medium armor reduces laser_medium damage by 26, so that's 11-21 points per shot or 33-63 for 12 TUs if you hit 100%.
Damage is adjusted for difficulty after armor reduction, and is a multiplier, not a flat bonus/reduction.
heavy laser: using pulsed fire, 15 TUs, 3 shots, laser-heavy, "52 6".
46-58, subtract alien medium armor damage reduction vs. laser-heavy of 24, means 22-34 per shot or 66-102 damage for 15 TUs if you hit 100%.
sniper rifle: aimed shot, 18 TUs, normal-heavy, "105 0".
105 pts, subtract medium armor DR of 22 = 83 damage for 18 TUs.
coil gun: aimed shot, 18 TUs, normal-heavy, "180 36"...
144-216 pts, subtract 22 = 122-194 points for 18 TUs
bolter rifle: 3-round burst, 14 TUs, normal-heavy, "75 10" -
65-85 pts, subtract 22, 43-63 x3 ~ 129-189 if you hit 100%.
submachine gun, 15-shot full auto, 18 TUs, normal-light, "20 4" -
16-24 pts, subtract 31 from medium armor = you do the minimum 1 pt per shot that hits
flamethrower: 60-shot Inferno, 12 TUs, fire_flamer, "6 2" -
4..8, less 3 from medium armor = 1..5 per shot that hits - 60..300 if you hit 100%, but average a very nasty 180.
particle beam cannon "Unrestricted Blast", 1 8-ammo-using shot, 28 TUs, splash damage of "210 20", particlebeam-heavy, blast radius = 4:
if at ground zero, damage = 190-230, less 24 point reduction from medium armor == you're still toast.
damage at 3 units away = 190..230 x (1-3/4) = 47.5..57.5, less armor reduction = 19.5..29.5.
particle beam rifle vs. nanocomposite armor, 15 TU aimed shot (particlebeam-medium), "90 15" --
75-105 damage, less 17 from armor - 58-88 damage.
plasma blade vs. nanocomposite armor, 7 TU 'lock' "300 5", plasma-heavy
295-305, less... 20 points, but it doesn't matter...
kerrblade vs. nanocomposite armor, 14 TU slash, "180 45" monomolecular --
135-225, less 12 = 123-213 points.
For reference, a Taman should have 100-130 health, Ortnoks 120-160, Shevaar 120-160, Bloodspiders 150, and your average new recruit 80-110.
As a side note (noticing this because they're in the same file...) 1% chance for any of your singleplayer-game recruits to be 'elite'... which gives them FAR higher starting stats. Strength 25-35, Speed 25-35, Accuracy 30-40, Mind 30-45, weapon skills 25-40, health 100-130. For comparison, other recruits will have 15-25 strength and speed, 20-30 accuracy, 20-35 mind, and either 15-25 all weapon skills (non-specialists) or 25-40 in one weapon skill and 13-23 in the rest.
Taman soldiers will have far higher stats (accuracy 40-50, weapon skills 50-90); what hurts their hitting ability is that they don't crouch much when shooting, and that they tend to have weapons with higher spread values.