The trailers hydraulic brake actuator is what dictates the incab controller requirements. Ford's factory controller has been out long enough that some/many brake equipment is now compatible.
We run almost all hydraulic disk brakes on our fleet of trailers. We converted a dozen older trailers (mostly 8K axles, some 7K axles, goosenecks and bumper pull....all equipment trailers). We have required all new trailers the last several years to be hydraulic disk. We have found the Dexter actuator
(http://dexteraxle.com/electro_hydraulic_actuators) to be one that works with most all in cab brake controllers including the Factory Ford control. We specify this actuator on new trailers we bid out.
I had a 2007 F250 with the factoy brake control, and now a 2008 F350. Both work fine with all our trailers.
BTW....once you have pulled a trailer with hydraulic disks, you will never go back to electric.
jjw
ND