Uh oh, sorry it seems I didn't make it clear enough, what I want.
I'll try rephrasing it:
The SDADC comes with a programmable gain amplifier stage after the MUX. That PGA has an offset and a gain. The offset is automatically calibrated during the SDADC init procedure and the gain is configurable to 0.5, 1, 2, 4, 8 and so on.
According to the datasheet, the gain isn't very exact, though. There is a typical gain error of -2.7%. And this is what I try to calibrate. I want to measure the gain error.
To do so, I use the very precise external 3V reference as reference for the SDADC. After doing offset calibration all that's left to do is measure another known voltage which is as close to the reference voltage as possible. By comparing the ADC reading to the actual (known) voltage, I can compute the real gain and then use that to do all following measurements with very high precision. This step is repeatable to account for temperature drift etc.
And for this gain measurement I want to use the internal, calibrated reference voltage as I presume it's going to be accurate enough due to it being calibrated and so I can spare myself from having to buy two precision resistors to get a second voltage.