I agree about using both liner and pack cover when the weather is abismal. And I agree with all the arguments in favor of liners, and I use them... just not alone.
I like a pack with lots of pockets and I use a poncho most of the time. The poncho does not make additional protection unnecessary, just redundant. Redundant is good. If I take the pack off, the cover protects it. The pack cover is also a water bag and gear hammock. When I get to camp, it contains the pack explosion as I unload everything. The liner (if I am using one) is still inside the pack and is of little organizational help.
In addition, while it is true that the nylon of a pack will absorb little water, the pack can collect and hold quite a lot. If the liner is compromised, water pressure inside the pack can force water through.
On the AT in '03, I used a liner, a pack cover AND a poncho. Anyone who was on the trail that year will understand that only redundant systems and careful procedure could keep anything dry in the record rainfall.