We typically start with a single map (as in document with appropriate doc control references). This will then be used to create all the subsequent maps for a job (save copy, change as required). Each output pdf/map will have a doc number and matching versioned project/aprx.
Pro likes to create empty folders everywhere for every copy of an aprx.
Please change the behaviour so all the noise gets saved in a sub-folder of the default folder. This will keep the job folder where the aprx & pdf files are saved uncluttered up with empty folders.
In a job with 50 maps (aprx + pdf) we now have an empty folder for each at minimum.
I am lucky that I work for myself but in a shared environment this is a nightmare to figure out what other people did.