Sean, when you hear about people shoving their bag into their pack, 98% of the time they also use a waterproof pack liner.
As per your question, I think it depends on how you like to pack. For me, I usually like an ultralight dry sack, like a cuben one. Sea to Summit makes good light ones in sil. That way I know that no matter what, my down bag is safe.
However, I just got a Catalyst and have been playing around with how I pack, and might be moving to a liner. Certain packs seem to lend themselvrs to being packed differently.
Play with many different ideas there's no right/wrong/better/worse way. But I'd suggest that no matter what you pick, make sure your insulating pieces (bag, puffy, etc) are very well protected from water.