Concussion damage is partially blocked by armor, while penetration damage isn't.
Unupgraded:
RailGun: Concussion Damage: 80, Penetration Damage: 40, Reload Time: 80
RPG: Concussion Damage: 60, Penetration Damage: 40, Reload Time: 55
Upgraded:
RailGun: Concussion Damage: 100, Penetration Damage: 50, Reload Time: 65
RPG: Concussion Damage: 100, Penetration Damage: 45, Reload Time: 55
Of course if you divide those values by the reload time (i.e. how often it gets to inflict that amount of damage):
Unupgraded:
Railgun: Concussion: 80/80 = 1.00, Penetration: 40/80 = 0.50
RPG: Concussion: 60/55 = 1.09, Penetration: 40/55 = 0.72
Upgraded:
Railgun: Concussion: 100/65 = 1.54, Penetration: 50/65 = 0.77
RPG: Concussion: 100/55 = 1.81, Penetration: 45/55 = 0.81
So as you can see, the RPG does more damage per unit of time. Also, for a weapon with a faster rate of fire, and lower damage, there will be less overkill. Which means you can switch to shooting up the next target faster, on average. (Say a vehicle only has 1 HP left, then 1 shot from either weapon will kill it, but the one with the lower fire power and higher rate of fire "wastes" less firepower on it, and starts attacking a newer target sooner).