You write that your system package has tip positioning of 25.4 mm. What does that mean? Is the tip that high over the sample?
The sample can be moved vertically 25 mm with respect to the tip. As samples are mostly quite flat, during a scan, only a short range is used.
The sample can be retracted for sample changing or the tip can be manually retracted 25 mm too. Both the manual and motorized translators mean that, with minimum fuss a range of sample sizes can be accommodated.