To be honest this is mostly a wontfix. Either you do use the postgresql-common integration tools, then we need to assume that the config files from pg_createcluster don't get broken. Or you don't use the postgresql-common tools and do everything by yourself, that's also okay. But mixing the two is just too brittle, as there are so many combinations that it's hard to impossible to test them all.
To be honest this is mostly a wontfix. Either you do use the postgresql-common integration tools, then we need to assume that the config files from pg_createcluster don't get broken. Or you don't use the postgresql-common tools and do everything by yourself, that's also okay. But mixing the two is just too brittle, as there are so many combinations that it's hard to impossible to test them all.