The PhotoshopToSpine version I got from here today: spine-scripts/PhotoshopToSpine.jsx at master · EsotericSoftware/spine-scripts
I'm not using any Artboards in Photoshop.
So I have 3 just layers: ship, left-thruster and right-thruster. The ship layer has some transparent part that is overlapping with left-thruster.

When I run the script and import the data into spine, something interesting happens. The ship is correct, thruster-right is correct, but thruster-left gets a copy of the ship merged into it.

(I've moved thruster-left down so you can see it)
I just cropped the ship to no longer have any transparent areas that overlap anything else, but the thruster-left is still merging in a copy of the ship.