I found out that you can get transparency to work with sr3pccloth shader. Make sure that you actually have alpha map plugged in in Maya\Blender, export the model, then convert it, selecting the s3pccloth shader for your material. Then open .ccmesh_pc file of your model in a hex editor, and search for a string of bytes 15 56 E3 E4. That's the shader's id, the next four bytes are another id or a checksum of some sort, and then next four bytes after that should be 40 00 00 00. Replace it with 41 00 00 00, and save the file. Now transparency should work.