I banged my head yesterday, thinking my modeling was sloppy, but now I see the problem is somewhere else.
What I did: simply extrude the top-left vertex to the bottom-right vertex of the cube, using the Snap during transform option, set to snap to vertexes.
In every case, there is a deviation of sorts and will happen on one axis (always the third axis, which should always stay at 0, but it deviates instead).
Does anybody know what's causing this issue and how to fix it?
EDIT: If I wanted to simply connect those verts, I could have done it just as easily by selecting them both and press "F" to create an edge. That is not what I wanted to do.
What I want to do: basically, by extruding vertices to other ones using the Snap feature, I was measuring if there were deviations in my mesh geometry, removing those extrusions after (with Ctrl-Z). The Extrude feature can easily be used as a measurement tool like that - even extrude a face toward a desired edge or vertex, to check how it sits in correlation to the face being extruded.
But with those deviations that happen even on the basic starting cube, how in the world can I use the Snap-to feature when it produces such deviations?