After runing the script the message show that you should change mysql to mysqli support even if the former installation is already using mysqli... this happened in 4.4.0 -> 4.5.0 upgrade
You are correct. eZ Upgrade does not check whether or not mysqli is already specified. Hence, this is marked as a feature request.
Variations of fixing this issue could be:
Make the message more generic (ensure you are using mysqli)
Check to see if mysqli is already in use
Change any occurence of mysql to mysqli. This would probably require a prompt beforehand to ensure that this is something the user actually wanted (and had support for).
After runing the script the message show that you should change mysql to mysqli support even if the former installation is already using mysqli... this happened in 4.4.0 -> 4.5.0 upgrade