>>320556735
I haven't followed that guide myself, but I feel like it's not that important to get the textures to look right in blender as long as the UVs are intact; all that matters in the end is how the model looks in unity.

skimming through the rest of the tutorial, I think you should just skip most of the texturing/atlassing stuff and get the model into unity first. It'll look bad, but you can work on improving the materials incrementally.