ClassiCube has a WIP GBA port, but according to commits it only hits 2 FPS as of now and is not listed in its README.
On a related tangent, there's also Fromage, a separate Minecraft Classic clone written for the PS1 (https://chenthread.asie.pl/fromage/).
In this case, the creator wrote a custom 3D renderer and recreated the models/meshes to get as close of an approximation of the N64 experience onto the GBA.
I wouldn't call it a port necessarily ("recreation" seems more apt), but it's closer to that than a demake.
Still bravo! I know getting it working and complete is the real goal and it is commendable.
What were you expecting?
One of the listed features in the PS1 port in the OP article is tesselation to reduce the issues of the PS1 HW affine texture mapper, on the GBA you have some base cost of doing manual software texture mapping but also oppurtunities to do some minor perspective correction to lessen the worst effects (such as doing perspective correction during the clipping process).
I think the resolution makes it particularly rough though.
Also flat shading (vs. say gouraud shading) is isomorphic to the question of texture mapping, and concerns how lighting is calculated across the surface of the polygon. A polygon can be flat shaded and textured, flat shaded and untextured, smoothly shaded and textured, or smoothly shaded and untextured.