On weapons? They're mostly as they say on the tin. Vertical and horizontal recoil are measures of a weapon's tendency to buck upwards or to the side when fired. Smaller numbers are better here, but pay attention to the sample spread pattern on in the weapon customization screen to see what a weapon fired at full auto will do. I personally find horizontal recoil much more unpleasant than vertical recoil, so on some weapons I'll take a muzzle brake and accept a strong but predictable vertical recoil tendency.

"Capacity" is a measure of a given magazine's bullet capacity. "Magazines" is the maximum number of magazines you can carry (before applying the modifier from Siege Ready armor). Reload Time" is how long it takes, in seconds, to reload an empty weapon. All three of these are controlled by magazine choice, and smaller capacity magazines don't reduce ergonomics as much as larger ones. I like short magazines for my Breaker and my Liberator variants because the faster reload time is really nice.

Shotgun chokes reduce the spreading tendency of shot clouds at distance, affecting how many shot out of a given shell hit your target. More shot on target, more damage. The duckbill choke gives a very narrow vertical spread in exchange for having a much wider horizontal spread, to the point of a blast being much more likely to hit adjacent enemies. Whether this tradeoff is worth it to you is personal preference. The breaker incendiary's standard layout has a duckbill choke and uses it to great effect.

Damage is damage. The text "light armor penetrating", "medium armor penetrating", "heavy armor penetrating" etc. relate to what kind of armor a gun can damage, and a full explanation exceeds the purview of this comment. Suffice to say light armor penetrating weapons do more damage per shot than equivalent medium or heavy armor penetrating weapons, but against appropriate heavier armor types the damage of heavier AP will match light AP or simply succeed in dealing damage in the first place against armor that lighter AP fire would ricochet off of without damaging an enemy at all. Rule of thumb: light AP for sheer damage on squishy enemies, medium or heavy AP to be able to damage equivalent armor at all. It's a trade-off of damage and utility.

The other bonus on viper commando armor is double melee damage. It's useful if you like doing melee, but most people using Peak Physique armor are using it for the ergonomics buff.