So to put it simple: this is just a bug. Or if not a bug then totally irrational function.
I would find it very useful if the Y-ruler would show me the Z-coordinates in the side view. It's strange that the Y-ruler is messed in the side view when using user origin since it has nothing to do with Z-coordinates.
Anyway, this was driving me mad since I thought that I was doing something wrong but it was just a bug. What a relief... Hope they fix this asap.