Capacitive sensor implemented on PCB - possible issues?
Maybe I'm missing your actual question, but I can't imagine why the addition of capacitive plates would cause any specific interference with the RTC. 

The capacitive sensor would be switching (for the charging time measurement), but that shouldn't be deleterious to your RTC. If you're worried, just place the RTC circuit away from the plates (more than 1-2 cm) and do a copper ground pour/flood/plane around it. The accuracy should not be affected by the capacitive sensor.