On a per unit basis, yeah, they get outdamaged.. but they're smaller.
Meson VI = 35 damage, 20kt
APB XII = 65 damage, 30kt
3 Meson VIs = 105 damage
2 APB XIIs = 130 damage
So at point-blank range, you give up 25 damage. Here's the interesting part- at max Meson range, you actually do MORE damage. But then the APB ship moves one farther away and you do no damage
It's similar for the PPB.
3 Meson VIs = 105 damage
2 PPB Vs = 120 damage, phased
15 damage this time. Again, the Mesons out-damage the PPBs at max range- but this time the opposing weapon can't fire from beyond Meson range. So against PPBs you can get away with max range attacks, assuming you have phased shields. Mesons are much cheaper to research than APB, too.
Phoenix-D