Can confirm the principle of least surprise being violated here. It took me 
getting a permission error trying to replace a file to test a bugfix to realize 
that:
- Commands without explicit permission elevation do system-wide modifications
- A theoretically user level setup is not fully covered by the backup of user 
files due to modifications escaping outside of the environment modifiable by 
the user
- Storage usage sneaked out of the expected scope (home of the user). Not 
meaning just installed programs, but ".removed" and "repo" added up to double 
digit GiBs, towering above the "app" and "runtime" sizes the user is shown 
during installation

The mentioned issues all stem from the problem that elevation is done with no 
notice and the usual barriers missing like either having to use sudo, or (worse 
case) being asked for a password instead of just denying the operation without 
being root.
However, circumventing the password requirement for privilege escalation 
presents an interesting dilemma:
- Either passwordless sudo is not a security issue as the user is expected to 
keep his account secure, and the additional obstacle of entering the password 
doesn't provide (much) security
- Or the extra step of requiring a password can be relied on as a security 
feature, therefore a combo of app-uninstall + modify-repo + app-install with a 
malicious repository could be used for interactive privilege escalation in some 
cases

Not completely on-topic, but as there's a divergence in privilege elevation 
here, I'll add an extra concern and question:
As hardware security key support is starting to look good, how will it be 
possible to use one universally for privilege elevation? As I understand, 
PolKit is mostly independent from PAM, so merely requiring pam_u2f.so for sudo 
as a second factor might not provide any extra security if PolKit would be 
still okay with just the password.
Can't say I'm a huge fan of PAM, but the centralized configuration surely seems 
to have an advantage, especially in such cases like this where a project is 
allowed to "slip" in rules lowering the security requirements for system 
modification.

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https://bugs.launchpad.net/bugs/1943480

Title:
  flatpak installation permission requirements different from ubuntu
  software

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