Below is a suggestion and some questions regarding profiles:
I frequently create tweaked profiles to deal with idiosyncrasies of specific prints. I manage these by saving the profiles with the objects ... usually there is a folder for the model, then sub-directories for G-code files and Profile files (since the profiles don't map one-to-one with the g-code. Then I use long names with home-grown conventions to try to keep things straight. This works OK, but gets confusing and complex as the revisions pile up with complex models. It would be nice to be able to discover, after the fact, which profile was used to generate a given gcode, and to understand the lineage of a profile.
Similar issues exist with multiple printers used for one model, each printer having variant g-code and profile files. Perhaps a management system for models/gcode/profiles would help. This seems similar in many respects to software configuration management systems; many of which are complex and confusing, unfortunately. (The problem itself gets complicated very fast and is hard to simplify with tools while preserving the freedom to change configurations and reuse profiles.)
Related to this is a question on the operation of the existing profile system. If I modify a profile on the FFF Settings panel, then save it. What is saved and where? Is the save only effective on the current profile as it exists in the computer memory? Or, does the save push the changed profile out to the file system, as well, so when the profile is used again, the save will be preserved?