Got it, thanks. Sorry I missed you are using WEBP with the texture packer rather than image export. I see the problems, thank you for the clear presentation.
We've fixed at least some of the issues in 4.1.29-beta. The WEBP failure the first try is fixed. Compression and other settings work now. I tried your skeleton JSON and atlas export in spine-player and it appears to render correctly. Clipping is respected. I'm not sure about additive and the draw order. The atlas shouldn't affect the draw order.
At any rate, please try 4.1.29-beta and if you have any remaining problems, we'll be happy to help! For the draw order we'll likely need instructions on how we can see the problem (eg which skin, animation, etc to look at).