hmm... sounds like you have misinterpreted their answer, though the answer was a little strange. They are talking about MySQL version. Unlike the MySQL extension, the MySQLi extension allows you to use MySQL 4.1+ functionality not present in earlier versions of MySQL.
Now, you asked if "is it easy for you to upgrade mysql to 4.1.3 or beyond (not 5 though!)". The answer given says that cPanel requires MySQL 4.1 or 5.0, and that you do not get a choice of which. Furthermore, the currently installed version of MySQL is 4.1.22.
The thing is, you want the version of MySQL to be "4.1.3 or beyond". 4.1.22 is the latest version of MySQL that meets your requirement, so ironically the answer, despite being an apology, tells you precisely what you want to hear!
What it does not say is whether the MySQLi extension is installed, so to conclude from your correspondence that it is not installed is jumping to conclusions.