As far as I know, the available open-source tools that are suitable for producing pixel art, are strictly flat-2D-only.
Not that you can't do 3D pixel art with them, but they certainly won't help you get there.
Edit: I just realized that maybe your question is broader than just pixel art. Open-source game development in general is a very underserved field; in terms of integrated game development environments, the best option I know of is Godot, and that's still miles behind a tool like Unity in terms of capabilities.
Audio production tools aren't great either, none of them integrate particularly well with the few game development tools that do exist. Good texture generators are difficult to come by; I believe Blender does have some functionality to this end, but it's not very accessible.
In terms of 3D modelling, Blender is decent, but suffers from bad UX (although that's being increasingly fixed, so that's great!).
I'm not aware of any production-ready general-purpose release/infrastructure tooling existing that's equivalent to something like Steam Workshop.
In short... there are basically almost no good, accessible open-source tools for game development, no matter what aspect of the process you look at.
I'm not sure how "stacked sprites" differ from voxels, since this appears to be the same technique Westwood used in it's voxel engine; but voxels are the traditional "3d" pixel art.
