On Debian 10 the issue is also visible, what we get is my.cnf from MariaDB which includes "mariadb.conf.d" directory which is empty, so basically no config is set.

I still think this is a big problem, you end up with mixed configuration - the old one is active and the new defaults are active too.
The my.cnf after upgrade includes all 3 subdirectories and same configuration options are available in multiple places:

If this is not going to be fixed, it needs to be documented that after upgrade on Ubuntu/Debian:

1. new defaults are available in /etc/mysql/mysql.conf.d/
2. the old configuration (unless user changed this before) is available in /etc/mysql/percona-xtradb-cluster.conf.d/
3. user should edit /etc/mysql/my.cnf to include only the directories that he really wants to use
^

Not only is the layout with included files somewhat messy and confusing. It contradicts what the upgrade docs at https://www.percona.com/doc/percona-xtradb-cluster/8.0/howtos/upgrade_guide.html state:

This only happens on Ubuntu, on a RPM system we got what the documentation says and what is in . The packages behaving differently is quite confusing and should at least be clearly documented. Preferably they should act the same way, I think.{{}}

   We need to add a note when upgrading from 5.7 to 8.0 that the configuration file layout has changed and configurations may need to be moved from old location to new.   If you have any questions,  ask

Yes I think we just need to document this properly. The same behavior we have in PS.