Zygmunt, that's unfortunate to hear if what you are describing is a
fundamental design principle of the snap ecosystem.

While I wouldn't advocate that a user customize their home environment
in a way that arbitrarily goes against convention and standards,
locations should at least be configurable for when there exists a good
reason to do so (and in $HOME, a good reason includes "because that's
how I want it"). In this case, the desire is better compliance with an
established standard that has become quite popular. That's a good
reason, IMO.

What happens under the snap folder is legitimately the business of
snap/snapd, but where it's located in the $HOME filesystem should be
configurable.  If not, it should be placed somewhere that is
legitimately manageable by the system and made accessible to users in a
way controllable by them (or possibly the system administrator).

As an aside, your description of what basically seem to be "hard coded"
paths for mounts and security policies explains a tangentially related
problem I'm having with snaps - on my system I use a non-default
location for $HOME, and that's messing up the 'carefully spelled out'
security policies, apparently.  That's a problem, because there's no
guarantee that $HOME will be under /home on *nix systems, particularly
on servers or genuinely multiuser systems.  Though technically
difficult, that possibility needs to be taken into account by the snap
ecosystem.

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https://bugs.launchpad.net/bugs/1575053

Title:
  User data directory should conform to XDG Base Directory Specification

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