> As far as I know, the available open-source tools that are suitable for producing pixel art, are strictly flat-2D-only.

There are plenty of voxel editors out there:

https://ephtracy.github.io/

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.