Well I will guess it has to do with who the CD store is using as a supplier/vendor. The "wholesaler" that they use may not have certain artists/labels available and you are probably right......It has to do with the designation of "domestic vs import".
I have asked several of my record store owners why they don't get vinyl issues of Porcupine Tree, SW, Genesis.....I think it is because they are not sure if they will sell. I asked about albums by Riverside for example ,CD or vinyl, and the owner could not find it on his "suppliers website".....again probably because it is an import.
The other thing is most of this stuff is available to the common buyer on the internet, my price is about the same as what the record store owner would pay and they know that.
Although I would pay a few bucks more just to know that if the record is damaged I can return it to the store much easier than if I had ordered online.....Sending things back purchased online is a major hassle.