Classic Traveller had the computers running programs such as the various Predicts and Gunner Interact verses the various Maneuver/Evades. I think the "relative computer" bit was intended to capture that in a simplified way - the bigger, better computer would be running the bigger, better attack or defense programs. Then there are the imponderables that you point out, for example the use of "computer" to capture such things as the effectiveness of targeting sensors, and possibly also the effectiveness of whatever the target uses to degrade or confuse your sensors.
We could of course argue the realistic simulation verses game bit, but in terms of game balance, there needs to be some sort of something to counterbalance the effects of computer bonuses, else the game simply becomes a slaughter decided by who shoots first. The game needs to be enjoyable as well as realistic, or people won't play it and all the effort toward realism goes to waste. So, in the interest of play balance and simplicity, we invent hand-wave reasons for the defensive computer to counter the offensive computer rather than sit down and design detailed and realistic - but burdensome - sensor/ECM rules and systems.
