Dave-Ror and I just got done doing this...here are the differences that we found:
(1) Coolant crossover pipe (under intake manifold) is different as drz400dude stated above. The AT version has an extra nipple on it that connects to the Transmission oil cooler. We replaced this with a MT Coolant crossover pipe.
(2) Coolant Nipple on upper oil pan (behind the water pump) that feeds the line to the Transmission oil cooler. We plugged this with a rubber cap and clamp. Note: there are also hard coolant lines that run to this fitting that need to be removed and replaced with the parts from the MT motor for the heater core hoses.
Pic of AT lines, MT only has 1
(3) AT Vacuum Pump on the back side of the passenger head. We removed this and installed the MT cam plate. (Note: there are 2 dowel pins pressed into the AT head to align the AT vacuum pump, these have to be removed before the MT cam plate will sit flush. We used the cam plate off the bad MT motor we were replacing.
(4) Oil line that feeds the AT Vacuum Pump on right hand head, we removed this and installed the galley plug bolt out of the bad MT motor we were replacing to block off the open oil galley.
(5) AT cars use a line from the vacuum pump on the back of the passenger side cylinder head to supply vacuum to the brake booster, the MT cars use vacuum created by the intake manifold. You will need to unplug the line fitting on the intake manifold and remove the line from the vacuum pump on the AT motor, swap the line from the MT car in it's place. Note: the plug removed here makes a nice plug to block off the coolant nipple in (2) above. Just be sure to secure it with a clamp.
The MT and AT engines use the same engine wiring harnesses per model year, 2013 harnesses only fit 2013 cars, 2014 harnesses only fit 2014 cars, 2015 harnesses fit everything 2015 and newer. Note: Subaru does sell updated harnesses for the 2013 & 2014 models that require the use of the 2015+ style coil packs.
The 2013-2014 engines use different oil temperature sensors, coolant temperature sensors and coil packs than the 2015 & up engines.
The only thing to be concerned about with the DI numbers is that all 4 installed in the car are the same number (They will be #1, #2 or #3), as long as all 4 are matching you will be good. The IDU doesn't care what number they are as long as they are all the same.