Add a local application to syslog excluded from /var/log/messages

Try replacing

*.info;mail.none;authpriv.none;cron.none                /var/log/messages

by

*.info;mail.none;authpriv.none;cron.none;local1.!=info                /var/log/messages

This will log message that match : any facility with level info AND facility not mail AND facility not authpriv AND facility local1 execpt when level is info.

You should use either

#My Custom App Logging
local1.*                                             /var/log/application.log
& ~

for syslog or

#My Custom App Logging
local1.*                                             /var/log/application.log
& stop

for rsyslog 7+ to prevent the log message from being processed further. Make sure this comes before the default rules which log *.* to /var/log/syslog.