> Are these features lacking?
Well, as I said I see them in flatseal so either flatseal is misleading or the features are there, and I have no reason to think flatseal is trying to deceive me so I assume they are there.
> I don't need any of these to access anything outside a specific directory (or a small selection of such, but I don't need them to access the full home dir, let alone the full root fs, even for reading).
Fire up flatseal and change the permissions to what you want it. I'm sure you can also petition for xdg-code directory or something and then keep all your code there and request the packages be changed to default only work under there but I suspect most people would not be so happy with this.
I am not sure how you expect the package maintainers to know where exactly on your FS you keep your code, I also don't keep mine in my home directory.
And maybe a blacklist would make sense, but if all that is needed is a blacklist then I would harldy say that flatpak failed because it is not really that difficult to fix that deficiency.
EDIT: Actually blacklisting is supported, see --nofilesystem in https://docs.flatpak.org/en/latest/flatpak-command-reference...
So really everything is there, maybe everything is not available in a nice neat UI, maybe the UX is not what it should be, but the core underlying system is not "lacking" these capabilities AFAICT.