I will preface by saying I am NOT using disc brakes, however do have a couple of suggestions.
Your IBC IS far superior to the likes of a "Prodigy", replacing with aftermarket would be a step down in brake controller.
Second, not sure when Ford added adjustment for Electric over Hydraulic brakes but you might want to check your controller menu to see if you have that setting.
Third, some of the Ford IBCs depending on your Trim package may also have additional adjustments which may allow you to backoff the aggressiveness of the IBC.
Fourth, if all else fails add some additional load to the electric brake wire, typically one or two electric brake magnets can be hooked up and mounted on the trailer tongue. The magnets load the IBC which may help the Hydraulic controller see proper levels. In a nutshell the Hydraulic controller may not be presenting enough load which results in too high of brake voltage.
Fifth, don't be afraid to back the IBC down lower, if braking is too aggressive, by all means drop the IBC level down. I have to do that when changing from TT to my empty open flatbed trailer which is much lighter..