Use cases
The main idea is multiple notes centered around a single changing entity.
I will list a few examples but of course the list cannot be complete because number of use cases is potentially limitless
Management projects
Project is always detailed with a lot of files that are continuously refined as more information is obtained
Consider construction project
Project details change based on market environment . Those project details (prices, contractors, headcount, inventory&supplies, CAD schematics, timelines, stages of completion, etc) are usually stored in spreadsheets, presentations, pdfs, CADs, pictures and many other proprietary formats.
If there's no way to link to a single file (for example representing headcount), one has to add latest version across all notes containing such file in past manually.
Suffice to say that managing projects in this way gets very tiring - because every change requires to update manually almost every note describing the project.
Programming project
Consider documentation about binary blob. Same as before, you don't want to copy latest version to every documentation page.
Design projects
Same as before, but instead of binary blob you have animation, video or interface file.
Corporate documentation
Organizational charts, descriptions of databases, minutes of meetings etc -- all of it is constantly changing
Zettlekasten notetaking
This popular notetaking method relies on links between knowledge points. Breaking link functionality would make it impossible to use it.
Templates
Linked resources are neccessary for reused templates
Linking to large files
Do we really want to keep a copy every time we link to 2GB video (lecture recording for example)?
Inconsistency in UX
From user standpoint it's confusing when resource could be updated only if notes are in the same folder.
Given the necessity to copy resources with links, linking to resource outside of its folder is not actually "linking" but "downloading a resource copy". Therefore, link is no longer functioning as an actual link but as copying interface.
That behavior breaks the expectations of users who is used to linking 2 things together. For example, you don't expect browser to spawn local copy for a website if you refer to it. Therefore, in my personal estimation 80%+ of computer users would report this behavior as a bug.