That supposes that you have a decent filesystem like ZFS and know how to configure it. I run ZFS and I can't even remember how to add a disk and increase the size of a storage pool without referring to the manual page or do a web search. And I only know where to look because I know I'm running ZFS. (If I'm lucky it is in the filesystem command history - I know people who have used ZFS for years who didn't even know ZFS had a command history).

And what if I unplug the disk and pop it into a different machine? Of if you decide to move to Windows?

I do a fair bit of photography. If it taught me one thing it was that if you design software for managing lots and lots of files that craps out if something spans a filesystem border, you'll have a truly miserable time. Photo editing software used to be like that.

I actually use Windows (and OneDrive) quite a lot nowadays. I have very little problem thinking of disk space as a sort of OneDrive cache at this point and basically you have different devices that are faster vs slower. And when that's the case detaching a disk just means removing a copy of the data.

But datasets in general on ZFS are great because you can just mount and unmount them at will. They're there on the disk, but if you don't need them they're not mounted. This is great if you don't want to accidentally modify some subset of data you're not working with. One of my favorite features of ZFS are the encrypted datasets where you can have chunks of data stored with different encryption on the sane disk and all the integrity and migration etc works without needing to decrypt anything. Which is also great because it means ransomware can't touch it. I do think it's useful to have some sort of "chunking" of the data like that which mostly maps to ownership. This data belongs to this client/project, that data belongs to that client/project, etc. Often those divisions have different use restrictions so I've found it great to isolate things that way. And again ZFS is great at this because you can just dump out the full encrypted datasets for handoff/archival or whatever.

But anyway I would point out that filesystem boundaries come from whatever the filesystem implements and exposes to the application. The only real issue with filesystem boundaries is that renames that move files between devices aren't possible. And that's an artifact of that filesystem's design needing to synchronize the hierarchy at a hardware level. If you could call up the same path and it comes from wherever it happens to be then it's not a problem. Like in OneDrive when you open a file that's only online and it needs to suck it down first.