Indeed ,you are right. The transponder sends altitude info compared to 1013.25 ,no matter what is selected on the main altimeters.
This is from a transponder description:
'The KT 76C displays Flight Level Altitude, marked by the letters “FL” and a number in hundreds of feet, on the left side of the display. For example, the reading “FL 065” corresponds to the altitude of 6,500 feet, referenced to 29.92 inches of mercury (or 1013 hP) at sea level. Flight Level Altitude represents “pressure altitude,” and should not be confused with true altitude.
Please note that the displayed altitude may not agree exactly with the aircraft’s altimeter when flying below 18,000 feet, because encoders are preset to 29.92 inches of mercury. An encoder’s altitude transmission is automatically corrected for proper altimeter setting by a ground based computer, to present the correct altitude to the controller."
And I think the source selector that I've talked about will select which static ram will be used in conjuntion with the barometric capsule of the transponder (preset on 1013.25 ) in order to display the pressure altitude.