By default it should be only saving changed configs. By default it ignores quite a few things, which are found under "Comparison Criteria".. You can alter or add things to this to make it ignore more things if you want.
How are you triggering RTCD? I think if you do it via Syslog it will generate an event whenever you go into "config t" mode. I could be wrong about that. Using SNMP traps instead allows you to be a bit more selective, but I'm not positive that even I have things right at this point.
If you want to use SNMP traps, you first have to enable them and allow for at least "config" traps to go to your server. Then in Trap Viewer you would need to go to "View Alerts" and configure your alerts for config changes.
I currently have my "Trap Details" set to the pattern "*CISCO-CONFIG-MAN*" and under Conditions I have "CISCO-CONFIG-MAN-MIB:ccmHistoryEventConfigDestination" to be greater than 3 AND "CISCO-CONFIG-MAN-MIB:ccmHistoryEventCommandSource" equal to 1. Then you set it up to execute the program like you did in the syslog side of things and it should work. Not positive I only have mine doing it when startup is configured or not, need to do some testing...
Personally I turn off the email warnings about config changes...