Tolerances are required to ensure that parts, and their fasteners, fit together within specification.
Tolerances are an inseparable part of fabrication. However well the choice of fixing methods is chosen, badly executed detail can undermine the intentions. We often come across badly fitted screws exposing unwanted areas, inadequate or over projected screws inviting frowned looks from prospective customers. Designers would do well in understanding the nuances involved in such details. Tolerances deserve the respect they need.
Example of a typical countersunk screw.