There's 2 major flaws as I see it, both can be addressed by changing layout.

One is the unit's texture map is laid end to end, and being units are almost always longer than they are wide/tall, this makes the map extremely long, forcing one to scroll endlessly between faces.

Two is the annoying clipping bug where units that are taller than they are wide are cropped, leading to part of the voxel above the cutoff losing it's colouring.

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I propose the map be oriented so that all the long axes are horizontal, left/right/top/bottom, followed by front/rear. Thus we can actually zoom in and view the whole map on a standard aspect monitor for easier (and more precise) editing.

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If the length of the voxel falls below the height/width, you could pad that face/frame with something like the shadow colour in the palette, so as to be a clear demarcation for size used.

A default margin of 2-5px drawn around the whole thing would also help when it comes to selecting or drawing at the edges, similar to whatever the margin is that separates faces... again using shadow colour would be acceptable if parsing a margin is tricky.