You probably have the par-focal distance correct, 45mm is the distance from the shoulder of the screw at the back of the lens to the focus. The numbers in your post will be the effective focal length of the lenses, which relates to the nominal position of optical middle of the lens.
The working distance from the face of the objective to the sample is very short for high power objectives Objective Working Distance | Nikon’s MicroscopyU. Typically it is less than 1mm for 40x and 100x lenses and microscope slides are 1mm thick. So yes, you do need to turn the slide over so that you are only looking through the coverslip. Long working distance objectives do exist, but they are much more expensive.
If you have samples that physically have to face upwards for some reason then you could consider something like the Upright microscope prototype.