If possible, repeat the test with a different pad and rotor. The fork is no doubt flexing, but it should flex back smoothly when brakes are applied evenly and then return smoothly when the brakes are released. If it is juddering back and forth, that suggests that the brake force is varying in an irregular fashon, which could be contamination of the pads and rotors, glazing, etc...
What kind of rotor is it? The hole patterns in some rotors are also prone to chattering or pulsation, even without contamination.
P.S. The fork certainly has some flex. It is unavoidable, and is even designed in, as most forks, particularly on endurance bikes, have for/aft "splay" designed in to smooth the ride over bumps. There has been some criticism of disc versions of popular bikes, with reviewers saying they feel harsher than the rim brake version of the same bike, which is usually attributed to the increased reinforcement needed to deal with the loads of the disc brake. Designers are trying to strike a very fine balance between stiff enough for stable disc braking, and flexy enough for a ride that isn't noticeably harsher than a rim version.
Rotors and pads are the stock Shimano items that came with the 785, so nothing special or exotic. I have not ridden the Endurace a lot since mid august, and the few time I went out with it, no chatter, but I didn't have any in 8000 km's before it happend twice. The new disc bike will be there 3th week of oct, I'm curius to compare fork stiffness between the Endurace and Addict disc.