By "store bought" I'm assuming a commercial, mass produced quilt. They are probably manufactured more for look than function. I'd say chances are a homemade quilt will be warmer than a commercial one.
In my quilts I don't use batting. I use quilter's flannel because my quilts are intended for additional warmth on top of your existing bedding. Plus they fold up small for storage. Though thin, my quilts do a good job of warming.
Comforters are a different issue entirely. Recently we bought one from IKEA. It's almost too warm!!