I found some hints to that speed issues in Atmel's doc11106.pdf, Analog-to-Digital Converter in the SAM3S4 (searching for such a document addressing SAM3X was not successful).
They say, that STARTUP is needed for SLEEP mode and Fast Wake Up (FWUP) mode, because the ADC needs this time to get ready for conversation from SLEEP (40 us) and from FWUP (12 us) to normal mode.
As far as I understood, in normal mode there is no need for STARTUP (value may be 0).
There is a formula to calculate the sampling frequency Fs with Fadc = 1/ADC_CLOCK (programmed via PRESCAL).
Fs = Fadc/(n(STARTUP) + Tconv) with Tconv = 20 (ADC clock cycles).
This has to be devided by the number of used channels.
n(STARTUP) is not linear, it is given as a list of values in the data book of SAM3X:
0/0, 1/8, 2/16 .... 10/640 ... 12/768 ... 15/960.
It looks like as other parameters (TRANSFER, SETTLING) happen with a channel while another channel is converted, so there is no influence on the sampling frequency. TRACKTIM is a delay between conversions and may be 0.
I hope, I've read the description in doc11106.pdf correct. If I made mistakes by repeating, someone should tell us the truth.
A correction:
SETTLING and TRANSFER is not overlapping conversion, only the Tracking. Look at Figures 44-2 and 44-3 (page 1333) in the User Guide of SAM3X. Seems, that TRANSFER and SETTLING is inluded in the 20 ADC clock cycles mentioned for conversion time.
But I did not really study all the text, may be, I'll do that later, now I want to make progress with my software.