If you have the stock shifter and stock trans oil, you should be in good shape and they should fix it.
I experienced "notchy" shifts into 1st and 2nd, but my dealership blamed it on my MGW shifter and didn't even look into this problem. I mentioned that there is a Ford tech bulletin for adding a friction modifier to the trans oil and that's all they did. This helped a bit, plus adjusting the MGW shifter adjustment screw. It's still a little bit "notchy" in 1st and 2nd, but I can (and have to) live with that.
I didn't want to change the trans oil, because of eventual warranty issues, as they may have a reason to blame it on the oil.
2014 GT Premium, Custom Painted, 401A, MGW, Brembo, Steeda CAI & 93 Tune
Steeda Sports, HD Mount Koni STR.T BMR Rod/Poly adj. LCA & Relos, PHB & Bracket
Forgestar Custom Painted CF10 19x9+35 & 19x11+42 Roush Grilles & Chin Splitter
FRPP Quad Axleback 3dCarbon GT500 Spoiler MMD Window Louvers SHR Fuel Door JLT Oil Sep.