"I just feel like I HAVE to be missing something big"
I suspect it's that there's not a very good relationship between a pack's weight, its carrying capacity in weight, and its volume, and that there's also a large range in various backpackers' gear density. It makes it hard to compare with others' experiences unless you match up all the details.
If I'm taking a synthetic quilt that I don't want to compress to death, a foam sleeping pad that I'm using inside the pack for support, a fleece for warmth, a Driducks jacket, and a bunch of crackers that I didn't crush first, I'm going to need more pack volume for a given base and food weight than if I have a highly compressible quilt of the same weight, an inflatable pad, more compressible outerwear and a ziploc of Grape Nuts.
If I have high volume and low weight, I might choose something like a Granite Gear Virga, which feels cavernous when I pack it. If I needed to carry a ton of water, but not a lot of gear, I might choose a relatively low volume pack but one that's designed for heavy loads - something like the Osprey Atmos 50 I used to have. About the same volume as the Virga, but easily capable of carrying twice as much weight (YMMV).
The cottage packs seem vary a fair amount in their density sweet spots, but in my experience, tend toward low-ish volumes relative to their weight-carrying capacity. (Interested to hear about counter-examples.) I'm guessing this is at least in part to avoid the half-full problems that the higher density users would experience, but that's what you're running in to. Other than getting more dense stuff or a higher volume pack (which need not weigh significantly more, as long as there's no feature creep), solutions include adding a longer extension collar and strapping stuff to the outside until food volumes shrink (with caveats related to bear can use).