I have no argument with you whatever, but there are significant consequences to running a referenced library and they should be expressed when it is recommended. There is a real risk of dataloss when the user becomes responsible for file management, and is not made aware of that. That was my primary point.
Also, frankly, there are some factual inaccuracies in what you post:
When Apple change the Pictures folder into a "package" in your Home folder, it made management of photos that much more difficult.
Apple didn't change the Pictures Folder to a package. Apple changed (first) iPhoto, then the Aperture and now the Photos libraries into packages because the libraries were being inadvertently corrupted by users. Again, a source of dataloss. There are no user serviceable parts in these libraries, and there never has been, right back to the first version of iPhoto, twenty years ago.
It is bad enough when you import into Photos that it creates a bunch of aliases, but it also creates thumbnails, which on the surface look just like the original. Then when you go to search for photos, you don't know unless you compare the photos side by side whether or not you are looking at thumbnails or original, and can find yourself deleting your originals.
It doesn't create an aliases. It did back in the early days of iPhoto, but hasn't in years. Secondly, these apps are Photo Managers. They are your go-to apps for managing your images - like Contacts us for your addresses and phone numbers. You don't search in the Finder for the file with your brother's email address, you search in Contacts. Equally, you search in Photos (or the many hooks into the app) for your photograph. It's the photo you want, not the file. It's quite the point of using these apps. So, no, you're never comparing versions because they're all in the back end - the place with no user serviceable parts. If you are doing this, then frankly, you've not grasped the concept of Photo Manager. When you refer to "real management" you seem to refer to file management. These apps make that redundant for photograph files. Import an image, It creates various thumbnails. Edit it and it creates a preview. Delete it and the original as well as all of these extra files are removed.
Attempting to interact with these libraries via the Finder or other file manager is a possible way to explain why you've lost data migrating.
This is true of all photo managers- iPhoto, Photos, Aperture, Lightroom Classic and so on. They are about managing the photographs and not the file management. If you want to manage files, don't use a photo manager.