I've had the chance today to play around with my setup today.
In regard to my questions above, I can report the following:
the igus controllers in fact seem to be happy with the "unadultered" output of the EBOB. They have a separate +5V/- input for logic level connection with external controllers such as the Duet, which I connected to the same 5V/3A PSU as the Duet itself. Accordingly I've only connected the S-, D-, and E- pins to the respective inputs of the igus D1.
I've gone with the recommended setting of M569 P5 T20:20:10:10 which in turn seems to work fine. I've not tried to go any lower yet (is anyone interested in this experiment?)
regarding resolution, I've set the Duet and igus D1 up at 1/32 stepping at the moment. Considering the 20T HTD 3 mm pulleys I am using resulting in ~ 106 steps/mm and at 25 kHz max. step frequency this gives about 235 mm/s in movement speed which is totally acceptable. Moving the one motor I'm experimenting with seems to work even at higher speeds. We will see in the final application how well this works.
I have checked the M122 B1/2 comand. The firmeware update I installed in September, didn´t install the firmeware to the expansions, only to the mainboard. Now I manualy installed the 3.2beta to expansions (with the M997 B1/2) an the mainboard. I keep you updated.