Continuing on . . .
I spoke to Atmel support and they told me that there is a problem with the TRACKTIM field and its implementation (“there is an issue with how tracking is implemented in the current SAM3X module. It is documented, that the TRACTIM time is extended to the next start of conversion. But the field TRACTIM turn to be useless, the track time will be always 15 or 16 cycles”).
They confirmed that values for this field between 0 and 14 always give a tracking time of 15 ADC clock cycles. While a TRACKTIM value of 15 gives a tracking time of 16 ADC clock cycles. These are the only values that can be obtained.
So, I plan to use TRACKTIM=0 and TRANSFER=1 and to change the ADC clock frequency to make sure that the tracking time is long enough (see the previous plot).