Indeed, individual photo folders (at least the managed ones, as opposed to the scanned folders) have the same issue and this is definitely a strong point to consider.
The implementation details of this vs. the way “individual photos” folders are manages differ quite a bit, though, and some features may not interact very well by default. For example, using an export collection to automatically export some of the event photos to a “publish” sub folder within the event would generally conflict with a rule to organize images into sub folders by day.
Another consideration is the “Mark Folders As Events…” functionality, which allows to quickly switch between considering a sub folder of a scanned folder to either contain individual photos or to be an event folder. With rules that have sub-event granularity that could mean that accidentally selecting a folder as an event could unexpectedly mess up an existing folder hierarchy. But maybe this could be solved with a per-event option that defaults to “don’t organize within event” for events outside of the library.
My gut feeling is that such a feature should probably behave selectively (e.g. specific to a certain file type or ignoring exported photos) and it should probably allow to specify multiple organization rules/path templates. This would then lead to the next question of whether it would actually make sense to offer this for individual photo folders as well, for example to enable storing all RAW files in a “raw/” sub folder.
A final thought would be whether this should also be extended to file names, or whether that’s really only something to consider for imports.
(I’ve opened an internal ticket for this (#1563) to keep track of it and will move this to the “Feature Requests” category)