Oh I see this is actually a asset from the ARK Devkit from ARK Survival Evolved, do I need to modify the file to be ready by substance painter ?
For the UVs on negative coordinates, you'll have to modify it in order to be Substance Painter ready, yes.
For the overlapping UV islands, this is something game studios sometimes do for optimisation, but it surprised me a little bit on the scope.

With that being said, there is probably a logical explanation and I don't know how it supposed to loook in game.
I let you enclosed the mesh with the right coordinates, but I left the overlapping UVs untouched. You can try it this way, but I personally wouldn't bake the scope.
Best regards,