Most Linux/BSD distributions seem to separate out "core" PHP extensions (those that are distributed with php source, not via peel) into individual packages.
So while PDO may not be installed by a plain `apt-get install php5` or similar, I doubt the now deprecated `mysql` extension is installed by "default" in those scenarios either.
Edit: this approach also means that the PDO extension in php.ini will be commented, because its loaded by a package specific ini file e.g. /etc/php/7.0/fpm/conf.d/* which are generally symlinks to /etc/php/7.0/mods-available/