Im not 100% sure they don't do this already but.
The tagging plugins, for example Tag Scene From Performer Tags, Tag Images From Performer Tags, Scene Marker Tags to Scene should all check for the "Ignore Auto Tag" on a per tag basis. This way users can use tags in those for managing their collection that you don't want copied over.
For example, i have a StashID set of tags per stashbox source, i tag the scenes with this but also the performers and studios. I obviously don't want these mixed up so an easy way to have it not be processed by these plugins like the ignore button makes sense!
This should have multiple use-cases in the end which could be useful for many.