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No, the game doesn't have to "know" anything. He's just suggesting that the mercs should only get the "BOMB PLACED" after a certain timespan.
Like, the bomb timer is 30sek., but the mercs not alerted until it reaches 20. That way, if a spy gets to the bomb silently, without the merc knowing, he will get those extra seconds as a reward.
This makes perfect sense

If the spy was aggro, however, the merc would be there right away, knowing that he probably placed the bomb.
This does not.  The game still has to decide if the merc knew you were there to give you the proper countdown timer.  How does it know that you were aggro?

The merc will suspect the spy planted the bomb, if he's agro, so he would find it even before the timer is shown. However if the spy planted the bomb stealthily, the merc wouldn't suspect it and would be surprised by the timer. The countdown is the same in both cases.

I still think that electric bolts would kick ass.  So what if it's unrealistic? 

Electric bolts that knock spies down? You have to be kidding me. How about we give the merc a lightsaber when he's berserking? So what if it's unrealistic?  ::)

Seriously though, it just doesn't fit.

people will be playing as fast as possible,  or stealthy as possible   which is why I understand they took out multiple speeds for CT.

And good players will play as fast as stealthily possible.  ;D