There are several ways of looking at alignment tolerances, including standard versus vector tolerances, as well as sliding velocity tolerances. The most used are standard tolerances, but which are applied differently for short flex versus spacer couplings. The best laser alignment systems will allow you not only to select tolerance types but also coupling types. For standard tolerances, keep in mind that the vast majority of true flexible couplings (such as gear, grid, elastomer element, or diaphragm type) have two separate flex planes. So do all spacer couplings. The difference between short flex and spool piece, spacer, or jackshaft couplings lies in the distance between these flex planes. Any time the distance between flex planes is greater than the diameter of the working flex plane, you are better off calling it a spacer rather than a short flex, from the perspective of achieving satisfactory alignment.
Keep this in mind when selecting coupling type, as it will greatly increase the alignability of the machines, and ease your job in the field. For a deeper understanding of the subtleties involved in these issues, it is recommended to attend an in-depth training course in laser alignment.