Meanwhile I've made some tests. I've unprojected the clicked window coordinates to get the workspace coordinates with a Z depth based on the pixel check.
The resulted coordinates are pretty precise when in the TOP view, but are not so precise when the coordinate system is rotated, just like how I expected.
When in top view it is really precise, I mean it is exactly at the clicked point, visually there is no difference,
but when rotated then the results vary, especially when it is rotated with a high angle then I often see a few units differences, like in the +-2 units range which is a heavy error, but is understandable with the near/far plane distances we use and with the 24bits depth buffer.
So, if I'm correct it will be still OK for you, because you are only interested in the top view clicks, correct?