That's just because PPB's happen to be the only weapon that skip normal shields only - there are other weapons that skip shields and armor (Nullspace Cannon), weapons that skip shields and only damage internal systems (Tachyon Projection Cannon, Shield Disrupter) and there's even a damage type that allows a weapon to skip all shields, even phased ones, but no weapon uses that - does it even work? It would be nice if phased shields prevented nullspace cannons, tachyon projection cannons, and shield disrupters from skipping shields, but unfortunately they don't
But if you did decide to mod in another weapon with the same damage type as PPB has (forgot what it's called, something like "Skips Normal Shields"), then it would also be blocked by phased shields.