The printer only understands X3G so whether or not you use USB or SD the printer still only understands X3G

If you use Repg to send over USB then RepG translates to X3G before it sends it. RepG is not a slicer it is front end to assist in slicing and talking to the printer. Makerbot Desktop is a slicer (IIRC though I don't use it) and it too converts to X3G before sending it to the SD card or to the printer directly over USB.