Not sure what you expect. PS isn't a 3D modeling tool and does not support any low-level mesh edit operations like genuine booleans, vertex merging and all that good stuff. You have to use a real 3D program for these things. All PS can do is hack together a few primitives, but it's not contiguous, clean geometry.
Okay. I thought I'd ask just in case, but I can throw these pieces into Meshmixer. Again, I check to see how much I can do with this program because it produces the cleanest Texture Maps. My next question would be how to maximize the quality of those maps if possible.