Thanks for using the tool, I'm really glad it's been helpful!
The issue with transparent tiles is that transparency is handled by the shader/material on your object, so if you want transparent textures you have to switch the shader settings on your GameObject from "Opaque" to "Transparent" or "Cutout", or switch it to a shader that can process transparent textures.
Really kind of you to want to credit me, thanks! I don't need a name credit but if you want to credit the tool, a note along the lines of "Made using Mesh Edit" or something in the credits like that would be amazing! Thanks again for the offer, I'm looking forward to seeing what you're working on :)