1) .. MySQL can't recover from a single access error.
.. and yet NFS will wake your server, only MySQL will not when you get into this state.
There is no difference in the wake-on-access module between the two and this problem can not come from there. It could seem like the MySQL (kodi-client) module itself gets permanently broken after a single connection-failure and decides to never try again, that could explain such behaviour. I did not think it worked like that but I will have a look in the code
edit : I find this
CLog::Log(LOGINFO,"MYSQL server has gone. Will try %d more attempt(s) to reconnect.", attempts);
2) .. logging a WakeOnAccess every "TimeOut" seconds .. keeping the server awake
There is no difference between Pingport setting and frequency of ping-tests made so I dont see how this has any significance. If your rpi keeps server awake by repeatedly connecting to it then there must be an add-on (or skin) that does something periodically. You need to figure out what that is and disable it or let the server stay on 24/7. Check the logs to get an idea of what may be causing the periodic connection.