The RPM packages default the percona mysql user to root. I understand why this is done, but it is not secure. The default user should be mysql, or some other user not to conflict with the OS (fedora/centos/rhel etc).
The typical way to handle this is with an /etc/sysconfig/mysql (or percona) file. Configuration options should be set in here, not the init.d file. The init.d file should just have defaults, but should be able to be overridden in the /etc/sysconfig/mysql file. Also, this file should be marked as a config file in the rpm such that it doesnt get blown away during upgrade etc. Typically the init.d file will get blown away/upgraded when doing an rpm update, so any such configuration options in this file will be lost.