Q:

Can apt actions delete/modify files inside exiting user home?

I somehow always assumed that when I run a command like apt-get install, remove, purge then at most apt might add configuration dot-files files to my existing local home (not even sure about that), but NEVER modify or delete any files there (without backing up).
Is there any such restriction or at least guideline?

A:

There are two issues:

Debian policy dictates how home directories are managed and properly packaged .deb should not modify anything in users home directories.

9.2.3. Non-existent home directories The canonical non-existent home directory is /nonexistent. Users who should not have a home directory
should have their home directory set to this value.
The Debian autobuilders set HOME to /nonexistent so that packages
which try to write to a home directory will fail to build.
10.7.5. User configuration files (“dotfiles”) The files in /etc/skel will automatically be copied into new user accounts by adduser. No
other program should reference the files in /etc/skel.
Therefore, if a program needs a dotfile to exist in advance in $HOME
to work sensibly, that dotfile should be installed in /etc/skel and
treated as a configuration file.
However, programs that require dotfiles in order to operate sensibly
are a bad thing, unless they do create the dotfiles themselves
automatically.
Furthermore, programs should be configured by the Debian default
installation to behave as closely to the upstream default behavior as
possible.
Therefore, if a program in a Debian package needs to be configured in
some way in order to operate sensibly, that should be done using a
site-wide configuration file placed in /etc. Only if the program
doesn’t support a site-wide default configuration and the package
maintainer doesn’t have time to add it may a default per-user file be
placed in /etc/skel.
/etc/skel should be as empty as we can make it. This is particularly
true because there is no easy (or necessarily desirable) mechanism for
ensuring that the appropriate dotfiles are copied into the accounts of
existing users when a package is installed.

See : https://www.debian.org/doc/debian-policy/ for details

HOWEVER .....

Installing .deb requires root authorization and packages can run pre and post install scripts that modify files in home directories in violation of debian policy or people who package .deb may choose to ignore debian policy.

So it is possible for .deb to violate debian policy and alter files in user home directories.
This is one of many considerations or reasons you should be very careful when installing .deb from outside the Ubuntu repositories.

A:

No apt installation, update, removal etc should modify files in users' home directories.  Not even dotfiles.
Files in your home directory should only be modified by software that you run under your account.
There are reasons for this:

Home directories are designated by the FHS standard as directories under the control of the individual user, not the system.
The install/update/remove scripts have no reason to know or care which users exist on the system and no reason to do anything specific for any specific user.
Any system-wide configuration for any software will go in a system directory (ie /etc).  Dotfiles inside user accounts are only for configuration changes made by a particular user.
It is not the system's responsibility to update user-specific configuration.  If a piece of software needs a change in the way they are configured that software needs to do the migration itself when run as that user, not when installed or updated.

