:) Yep, I'm attempting to use those sprite slicers now and that's where I'm running into inconsistencies. For level design in 2D games a common approach is "tile-mapping," and one of the golden rules there is to pick a uniform tile size and then stick to multiples of that for your larger sprites.
When things are uneven numbers, or not multiples of one another, it gets much harder to lay them out on the grid. You can bail out of the grid system, but this creates a new set of woes in 2D games.
Of course, this isn't your fault. MagicaVoxel only knows how to export sprites at the canvas size, and certainly isn't built for creating grid-based sprites. Just something to be aware of when converting 3D assets into sprites.