MySQL: mysqld_safe options
I believe Percona already has that option built-in.
Inside /etc/init.d/mysql, somewhere I saw something like
# numactl --interleave=all

When I discovered this, every time I installed Oracle's MySQL, I added that command to /etc/init.d/mysql.
If you want to be sure, just run this:
grep -n &quot;interleave&quot; &lt; /etc/init.d/mysql

and you will see which line that appears.
I have discussed this before

Jul 22, 2013 : MySQL 5.5 High CPU Usage
Mar 06, 2013 : mysqld_safe version different than mysqld?
Dec 30, 2012 : Mysql slowly uses memory until it starts to use swap

Based on the link you posted, you should be able to activate those features starting from Percona Server 5.5.28. My posts mentioning numactl were evidently from earlier versions of Percona Server.
In light of all this, the same thing applies to flush-caches.
UPDATE 2013-08-28 09:54 EDT
If you have Percona Server 5.5.30 and there are no options, go install Percona Server 5.5.28 or 5.5.29 on a Dev Server and test it out there. Check /etc/init.d/mysql as follows:
# grep -n &quot;numa&quot; /etc/init.d/mysql

If you find it, then Percona must have missed putting that option on 5.5.30 (which would be very surprising). As the quick fix, take the mysqld_safe line from 5.5.28/29 and hardcode it into the mysqld_safe invocation in 5.5.30.
At the very least, take the line you said works:
mysqld_safe --datadir=/mnt/data/mysql --pid-file=/mnt/data/mysql/db3.improve.pid --numa-interleave --flush-caches

and imbed that into /etc/init.d/mysql for 5.5.30 where mysqld_safe is called.
I hope that human error (Percona missing this one (highly unlikely)) is the reason from this problem and not something much deeper.