flatpacks falling flat, packing bugs, snaps snapping resources, both suck

1. The "files referencing other files" issue I've already mentioned
2. Making it much harder for cli-only applications as they usually don't use GUI libraries such as Qt, meaning there's no easy way to shove portal-like functionality in there without having to adjust your code — but I may be wrong here; I simply have never seen it (Flatpak is very much tailored towards GUI applications; as a matter of fact you cannot package cli-only applications as Flatpaks properly)

There are two other sandboxing systems out there that I know about tangentially: Android & systemd. I know little about Andoid, but what little I know seems to be a two-part system: an application always has access to its own private piece of land within the file system that no other application has access to, and you can grant it access to the rest of the non-system parts of the file system via Android's permission system. It's not as fine-granular as Flatpak's system but requires much less interaction. It benefits from the fact that Android itself has a rigid design that it can impose on all applications, unlike generic Linux systems where users can store files anywhere, really.

systemd's sandboxing system is quite fine granular as you can set up certain paths to be read-only, others to be read/write, restrict capabilities etc. However, this setup is required before the program is started, meaning the admin has to know in advance which parts of the file system will be accessed in which way. This works fine for well-known daemons; it doesn't work so well for applications dealing with general user data such as LibreOffice or my own applications. In my case users often have stuff in their home, or on mounted network shares, on in places such as /data on different partitions etc. etc.

Again, I have no solutions here. This is a hard problem. Maybe there isn't a good one-model-fits-all solution at all, though I hesitate to say that as I certainly lack the knowledge in the area of sandboxing techniques to make such an assertions.

Maybe I'm just a bit annoyed with statements such as "<sandboxing technique> apps are more secure as they limit what the application can access". Yeah, it's partially true, and I'm probably just an annoying nitpicker.

If by "fundamental" you mean "a real pain in the proverbial for the user", then I think it is. Unless you comprehensively think through all use-case scenarios (which imnsho most developers are cognitively incapable of doing) you are going to have quite a horde of users complaining "my use case is broken".

For example, something I do, for very simple and good reasons, is have a humungous load of hard links all over my system. Less so now, but my wife and I took loads of photos (my camera tells me it can only store 1100 photos on the 100GB of flash cards in it ...) so they were all stored in a central area, owned by root (to prevent accidental damage), and linked everywhere they were required. Niche usage, sure, but most apps don't have a clue about that sort of setup. And there'll be plenty of other niche cases out there ...

Cheers,
Wol