Hey Yorgo,
The unused space is actually a small bug I noticed where textures were being unnecessarily doubled in size. This'll be fixed in the next update, which should be coming sometime in the next week or two.
Regarding the UV overlap, it's the most effective way of texturing the model. Because of the changes of colours, without the overlap, textures could grow to be massive sizes with a lot of duplicated information. So unfortunately, I can't really do anything about that one.
Hope this helps!