We are using a custom machine built with industrial automation gear. See the Studio Kite / Cadzilla article on your page.
I use a seperate command for fan on and fan off. Worst case scenario I will just post process it. It is not ideal though.
I am using a E3D tool changer, which requires changing the ALL of the commands listed on the old Firmware Configuration->FFF window. Without the ability to change these settings, S3D v5 will not work for the Duet firmware with multiple extruders.