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.
Please consider adding your weight and experiences to the existing ideas on the links below. The more ESRI hears how annoying/illogical and undesirable this beheviour is, the more chance we have of getting it fixed:
https://community.esri.com/t5/arcgis-pro-ideas/stop-recreating-missing-geodatabases/idi-p/1010302/pa...
https://community.esri.com/t5/arcgis-pro-ideas/arcgis-pro-2-4-2-why-the-arcgis-pro-creates-gdb/idi-p...
I strongly support this suggestion. This messy folder structure is by far the biggest barrier that held us back from transitioning from ArcMap to ArcPro sooner.
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