I don't know if this is the first thread that addresses the change in Kato coupler mount height....but the problem reared its ugly head at the end of my tenure at Kato USA nearly 20 years ago!
I provided full documentation on the M-T coupler dimensions and recall the meeting where I pointed out the factory error...leadership did not want to see that and kept on looking at different dimensions that were not a problem.
I don't have copies of any of the documentation but the factory made dimensional errors in the coupler. Rather than admitting their mistake, they decided to change the coupler mount dimension on all subsequent loco and rolling stock releases. (Lower the river rather than raise the bridge).
Micro-Trains was likely never informed of the change.
Charlie Vlk
I don't think that back then MTL actually designed any of their couplers specifically to fit Kato locos. As you mentioned, it appears that Kato designed their coupler pilot opening and mount to easily accept the standard MTL coupler box (1015 and 1016), except they did mess up the mounting height. IIRC, the 1015/16 couplers predate Kato pilot mounted couplers.
I recall that Kato's loco pilot coupler mount design goes back to when they first introduced the pilot-mounted rapido couplers. Then later they replaced the rapido coupler with their knuckle coupler. I don't know if that change required mounting height change, but I don't think so.
I wonder if the mounting height of the pilot-mounted Kato couplers dictated by the height of the truck-mounted knuckle couplers Kato uses on their passenger cars (and not purposefully to be drop-in-fit for MTL conversion)? After all, the pilot-mounted Kato knuckles perfectly match height of the truck mounted Kato couplers in passenger cars. That might be why they ignored Charlies warning adaptability to MTL coupler conversion.
I do agree that it would be nice if MTL came out with a coupler using the existing parts, which would be a drop-in fit for Kato locos. Like jagged ben mentioned, they already have all the existing parts that are needed (1015 shanks in 2004 boxes).