what!? ofcourse there is unit specific damage.
The Arclite Siege Tank isn't terribly effective at first. Its good range and damage infliction is offset by its poor speed and slow rate of fire. What's more, its explosive rounds only deal half their normal damage against small, lightly armored units like Protoss Zealots and Zerg Zerglings, who can easily swarm, surround, and destroy a Siege Tank in no time.
Source :
GameSpot:Video Games PC Xbox 360 PS3 Wii PSP DS PS2 PlayStation 2 GameCube GBA PlayStation 3
And all the siege weapons in the game can only attack ground units, which is a huge disadvantage along side their slow speed. if u have a single protoss zealot with full armor and shield upgrades, or two or three base zealots can easily take out a siege tank in siege mode. The protoss siege unit, the reaver iirc, is absolutely usless even in numbers if undefended IMO.
Even the uber air units have their weaknesses. the terran battlecruiser is so slow and its rate of fire is a huge handicap against faster firing anti-air units despite its armor. the protoss carrier can be taken down by six lowly zerg scourge (add a couple more to make sure the six hit).
And this brings me to the second point. The time it takes to get the upgrades and buildings that allow you to make these flagship units, even if u have all the resources
already on hand (which is never the case) is so long, that the opposing team can form a gigantic army of base units, say marines with stimpacks, or zerglings with hyrdalisks, or zealots with dragoons, that even a
couple of flagship units wouldnt stand a chance against. the zerg's unique building and unit construction method is perfect for early shock and awe tactics, while the protoss, though slow to build, their ubiquitous shields make them terrifying to face even in small numbers.
And all this doesnt even include the range of tactics that become available to you with specialized units like the science vessel, queen or arbiter.