I guess anything is possible.
If it were me and I've been in your shoes. I would check to make sure the PHS documents are real, not copies that someone could have swithced the VIN on the papers. Then I would pull of the AC box and check the VIN on the firewall to make sure it matches my dash VIN and title. If all of that passes then I would say you had someone who did a good job swapping out the ttops for a hardtop. I just picked up a Hurst install kit for mine. Came with the mounting hardware, ttop bag, owners brochure and install instructions. Best part is the frames and everything are black so they were intended for an SE to begin with.
I wish you best of luck and at least you know it's not uncommon for someone to swap out the roof