Weird Deviation using Extrude and Snap to

Here is the problem…

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).

This here is the starting cube. I did create another cube (with radius 6.3) and weirdly enough, there was no deviation problem with it! Made a cylinder after that and here we go - same deviation problem.

Does anybody know what’s causing this issue and how to fix it? I hate deviations!!

Isn’t there no logical explanation for this?

I am getting frustrated, all the answers I got in stackexchange were not any bit helpful…
How come there is a deviation like that, even on basic geometry like octagonal cylinders and basic square cubes?