Even if you had access to the DS hardware in GBA mode, the game doesn't look for the RTC on the DS, it only knows how to use the RTC if it was there on the cart only.
If you really want RTC that badly use gba exploader and the M3 GEP to play the pokemon, you wouldn't have to patch the games to use the RTC that way. As for transfering you will end up using the 3in1 anyways.