Hi Phasewalker. I wanted to drop in to tell you that these abilities aren't broken. Considering your small sample size, your numbers are actually quite accurate.
I'll go step by step as to why that's the case, but if you're a TLDR kind of reader: operation training dummies have armor that gives them 35% kinetic and energy DR.
The tooltip says that on average you deal 1804 kinetic damage with Tracer Missile, and you found that on average, your Tracer Missile inflicts 1410 kinetic damage. You include that this is with 5 stacks of Heat Signatures and with High Velocity Gas Cylinder running.
In this test, you ignore 55% of the target's armor rating. 20% from Heat Sigs + 35% from your Cylinder.
Operations training dummies have 5814 armor rating (not visible to you), which translates through our armor formula to about 35% DR. With your setup, you cut that armor rating down by 55%, effectively turning it into 2616 armor rating. [5814 * 0.45 = 2616] 2616 armor rating translates through our armor formula to 19.5% DR.
Therefore, an average Tracer Missile would deal 1804 kinetic damage, and a target with 19.5% DR would take 1452 kinetic damage. [1804 * 0.805 = 1452] This is only 3% different than the 1410 you reported, which given your small sample size is well within expectations.
The same methodology above applies to your Heatseeker Missiles. The tooltip says they deal an average of 2194 kinetic damage. Since the target has 5 Heat Signatures, that HSM deals 2632 kinetic damage. [2194 * 1.2 = 2632] Cutting through the same 55% armor rating as before, the target still has 19.5% DR, meaning that on average, your HSM inflicts 2119 kinetic damage. [2632 * 0.805 = 2119] This is only 1% different than the 2145 you reported, which given your small sample size is well within expectations.
All tooltips in the game show damage dealt, not damage inflicted after armor. Our tooltips do not show you the damage the ability will inflict after the target's armor.
I hope this clears things up for you guys. To the best of my knowledge, these abilities are still working as intended.
Perhaps you need to reassess the damage output of these classes then, because in the eyes of most players Commandos are sub-par. Whenever I see them on my scoundrel/vanguard/marauder I know its a free kill and can shut them down without taking more than 20% damage. I would also never willingly bring them along in my premade.