Good points.

I agree it doesn't look like there is a second floor, but there are clearly stairs on the side of the building leading to something. Maybe it's a set back second floor or maybe Lynch is just f-ing with us, again. I'm guessing the latter.

I actually think that 1945 version of the convenience store may have an above afterall and be the same store Mike and Bob shacked up in at some point. If you look over to the right of the building during the hobo walkabout you'll notice a set of stairs attached to its side.