I don’t know exactly how blender works, because i use maya software. But this look’s like you made a planar map to all uvs face from X, you need to cut uvs edges to make a appropriate unrwap. Try to cut edges and separate all this faces before unrwap, and after you do unrwap you can sew this faces.
using edit mode to modify things is the proper way to do things. you may need to explain a bit more on what you did. Did you modify the selection color in the preferences? what type of unwrap did you do? did you mark seam or something else like mark sharp?
I’m not sure what you mean mean by unwrapping onto a texture.
Regarding object mode scaling, I might have done that. I copied a different object and scaled that instead. That could be the reason. I’ll try creating a separate cube later.