The reason you need to know this is to find out what kind of reach you need to hit your target. You need to know what the distance is going to be from the base of your positioner to the center of your target, also known as the reach. You also have to remember to calculate your needle length in as well. If you are planning on running active probes, like the Pico Probe® 12C or similar or even Co-Planar probes for multi-contact probes, you will need to know the length and drop for them to calculate into your configuration.
This will determine the drop or rise you need to calculate into you configuration. Probe stations come with the chuck below the level of the platen as well as above the platen, there is no standard.
Magnetic bases are probably the strongest, but they can be a little harder to move. Vacuum bases are easy to move (by releasing the vacuum via a valve), but sometimes you give up grip strength. Hard mounts are also available where you actually bolt the positioner into place, but if you need more movement than the travel of the positioner, this will not work.