A problem Ive been dealing with for 8 years now
I'm trying to think of a quick way to explain it... so bare with me (it took me about 20 minutes to write this).
1. PHP can only be linked against a single mysql client library (5.0, 5.1, or 5.5)
2. If you link against a 5.5.x mysql client then the system will require that to be installed when php is installed
3. Some people might not want mysql 5.5.x, so the package is linked against the native version (5.1 in your case)
Result: Packager (parallels) links against the native client library, so a mysql upgrade isnt required when you upgrade php. For the packager, this design involves the least amount of work.
There is another way around it, but can cause other downstream problems for the packager. You link the package against the newer client (5.5.x), and then provide compatiblity libraries that live outside of the mysql-* packages to handle the condition where the system has mysql 5.0 or 5.1. This means that php is using the mysql 5.5.x client, and connecting to a 5.0 or 5.1 server. It works fine against mysql 5, 5.1, and 5.5 servers.
Ive bounced back and forth on this with the Atomic packages over the years. In the end I opted to link PHP 5.3.8 against mysql 5.5.17 and then provide backwards compat libaries for 5.1 environments.
So to your question, does this client mismatch affect operations. For the vast majority, no. Its going to be fine, where you would run into problems are with higher level mysql operations that phpmyadmin uses. So the warning is valid, at least when you're dealing with mysql 5.5 databases (if you had this on 5.0 or 5.1, its not an issue). Especially if you're still on mysql 5.5.14, there have been a number of very important bug fixes that resolve some of the nastier outstanding issues with innodb in 5.5.x.