Let me back up and start from the beginning.
So here is my sprite animated in Spine
Now after some tests, I found that the best look for this animation is what it looks like as an animated gif, 100% size and at 6fps.
Here is currently the Spine animation playing in my 3D game engine where it looks, as expected, the same as the animation in the Spine software.
The idea is with pixel art, you don't want it to be smooth like it is in the non-pixel view of the Spine animation. But chunkier and with fewer frames like it is when exported as a gif.
So I the goal here is to have the animation in the game look like it does in the exported gif. The fact that my game is in 3D adds another layer of complexity.
Update: Step 1 Complete
So I've successfully imported and run the spine animation in a 2D environment such that the animation in the game engine matches perfectly the animated gif I exported from spine. So this is exactly how I want the spine character to look. But I want them to look like this in a 3D environment. Next step is to project the drawing onto a rendertarget.
Update: Finished
It's working. I draw the spine animation in the bottom center of a 398x224 render target. Then I project that render target onto a plane. The plane rotates to always face the camera too of course. Also I have the render target created and updated every 6 frames to give it a more crunchy pixelly movement. In the video you'll notice how there is no "subpixel" movement in the animations. With each frame of animation the characters pixels translate at distances that match the pixel size of the character.