So I have been designing PCBs, and when I have a through-hole part, I have been placing the part reference inside the box that joins the pads to denote, for example, the terminals of a resistor or capacitor. I do this so that the references don't take extra space and therefore try to keep the PCBs small and costs down. However, it means that after the part is installed, the reference is covered by the part, and a map of the PCB which shows the references needs to be used to find where a referenced part is.
On the other hand, the reference could be placed next to the pads, and not inside the box joining the pads, so that installing the part does not cover the reference. The problem I have found is that if you have a high density of parts, it's not always obvious which reference goes along with which part. Then the parts need to be separated even more so that it is clear which reference is associated with each part.
So any opinions around here about if it is too much trouble, or too error prone, to require someone maintaining a board where the components cover the references to use a map to find the references?