"sandboxing" php-fpm
with libapache2-mod-php it is possible to use open_basedir to restrict access of phpmyadmin to files which are necessary for the software. This is not possible if phpmyadmin is running with fpm/fcgi.
This could be achieved by creating a systemuser which is used to run the php-process for phpmyadmin. Maybe we could ask the user if he wants to do this with debconf.