He's referring to Alpha Strike, where there are no pulse or targeting computers at all.
The effects of Targeting Comps and Pulses are taken into effect though, they're just rolled into the damage amount. You have to consider that both those bonuses only affect some of the weapons. Take for example a hypothetical Vulture Prime that has a targeting computer. It would have Pulse weapons, and a Targeting computer that would help target those lasers, but it also has the 2 LRM 20's that aren't effected by either a pulse or tarComp bonus.
The Vulture Prime has base damage of 4/4/4 and weapon abilities of LRM 1/1/2 and IF2. IF2 is exclusively for Indirect Fire (That almost nobody uses), and the LRM ability is basically for Ammo tracking on campaigns. (Remember that abilities are subtracted from the damage amount when they come into play in AS as opposed to the old BF rules that added the ability). If your potential pulse/tarComp rule was added in for a regular non LRM/IF ability attack, how would you reflect that the LRM part of the 4/4/4 damage values doesn't get the plus 1/2? (As a Vulture pilot I usually fire 1LPL + 2 LRM's to maintain heat, how do you reflect that?)
Two rolls you say- but...
From my inferences of questioning the AS rules it appear the whole guiding principle of AS is "
One Roll to Rule them All" that's why you can't do physicals AND weapons fire in the same turn... that would be 2 separate rolls (which also means nobody uses the physicals anymore... at my games this is allowed as a house rule). The core design principle of AS is a single roll for all attacks, one roll per unit, then the turn is done.
Yes the +1/+2's would be nice, but would mean multiple rolls, so they compromised and rolled the ability into the damage potential... Yes this gimps the ability a little bit, but it was sacrificed in the name of round speed, and you still get some positives out of it.