And with turning Voxels into elements you usually also turn the terrible performance that Voxels bring with them into Minecraft Models.
As long as you do the models properly, convert them properly and maybe do some cleanup work afterwards it shouldn't be a problem though.

(Honestly, some people ...

Simply said, more then 90% of Voxel engines don't support transparent voxels because it would prevent way to much possibilities for optimization.
If you want to make Minecraft Models, then don't use voxels at all but elements, voxels models in MC are usually terribly optimized.

While it's kind of good looking, it's a terrible model.
https://puu.sh/As9kn.png
This shouldn't look like this, in no case! (way to much vertices and triangles!)
That's a perfect example why the voxel function in Cubic is terrible, because people don't know how to use it properly.

Edit: At least ...

Why does Optifine need to make a feature that already exists within Vanilla? *shaking head*
The suggestion is to add support for it to Cubik, not to make it manually.

Meh I always mix up the names for the cases
Sorry for the mistake

2) is kind of wrong, java convention is camelCase
And SnakeCase for Class names (alias the java file name)

Issue #1 (quote from the java models suggestion thread):
You can fix it by substracting the model position from the rotationPosition for each element.
Issue #2: Entity Models are for some reason upside down D:
But this can be fixed either in code: GL11.glRotatef(1f,0f,0f, 180F);
Or trough exporting ...

Could you then maybe think about adding also support for the blueprint format?
(A more mod friendly version of schematics http://dark-roleplay.net/other/blueprint_format.php)

With enough skill of course.
Probably gonna be more work, but it will be definitely better for performance.
(Just for your information, the elements are the only supported format by Minecraft and voxels are converted to a bunch of elements. In case of the M40A3 I would say a few thousand)

This are Java Models they work completely different then JSON Models.
Basically they don't have any limitations at all (expect not allowing floats in element size and good uv mapping...).
Beside the fact that Tile Entities are worse for performance then normal blocks (all the render issues seen on ...