NijiNeko
Until I can see a comparison between the actual and expected results, and have access to one of your assets, my ability to help will remain limited.
In spine-pixi-v8, straight alpha / PMA is automatically read from the atlas file—there’s no need to set it manually.
You can adjust the min/mag filters by editing the filter values in your .atlas file. See here for how Spine filter values map to Pixi's.
If you prefer not to modify the atlas file, you can override those values directly on the Pixi textures, as mentioned earlier.
I don't quite understand how to control the shader, I lack knowledge in this area.
Shaders aren’t simple toggle settings, they’re actual GPU-side programs you have to write. Modifying them requires a good understanding of graphics programming and could impact your game’s performance, since a custom shader must be used to render Spine skeletons.
