I think your missing the point that the MKC is available with
a base 2.0 FWD or AWD @3000# trailer rating or
MKC with an optional 2.3 AWD @2,000# trailer rating (both with trailer tow package). All my spec comparisons are 2.0 AWD-to-2.3 AWD because the 2.3 is not available in the FWD MKC....
.... Seems the 2.3L is based off of the 2.0L. So the engine block overall is the same. Maybe more bore or stroke I don't know. But they might not have done much for the cooling system to change it. Or that .3 liters doesn't mean more durability. Or they revised their thoughts on the engine. But there is higher output which means more heat generated. If you tow with it you are in "boost" a lot more and that generates more heat. There just might be some shortcomings with longevity. Quite a few possibilities.
Here's a fact-sheet on the "all new" 2.3 as in the Mustang.
The MKC version has all the same features, just 'detuned' to 285HP/305 lb-ft. Maybe similar to the 2.0 in cylinder count, from what I've read most of the significant details are different, there are no interchangeable parts to speak of and the 2.3 has lots of unused 'overhead' for future power growth (the 2.0 block is sand cast, the 2.3 is die cast yielding higher strength for the 2.3).
.... Also, what size are the brakes? Towing needs bigger brakes. The MKC brakes might be smaller. (though this seems least likely)
Well, since they sell the 2.0 MKC with brakes adequate for a 3,000# trailer, seems likely they'd offer the same or better brakes on the more powerful 2.3 version (?)
... Also, being a Lincoln they have more comfort and an adjustable suspension I'm think. Softer spring rates or adjustable ones means that changes the dynamics of the vehicle. A trailer would only amplify anything with all that added weight being towed. The dynamics are the most important thing when it comes to towing. It affects stability, acceleration, cornering, braking. So they might not deem the suspension to be as tough as the FE.
Again, Lincoln makes the suspension work for a 3,000# trailer with the 2.0 engine in the MKC, so why not the same for the 2.3 engine?
I scoured the 2.0 MKC vs the 2.3 MKC specs looking for some difference that'd rationally explain the 1000# lower GVWR for the 2.3 and I can't find it yet. Wheel size, tire size and final gear ratio are all identical. RPM for max HP is identical, RPM for max TQ is about 10% lower for the 2.3. Curb weight difference is negligible. There's a rational answer somewhere and it may be one of the factors you mention but darned if I can hone-in on it.
Even wondered if its simply an error on the website but the same limits are in the Fleet towing guide and MKC owners manual, so scratch that.
One 'missing link' (and perhaps the 'weak link') is info on the power handling capacity of the tranny, which is the same 'model' for both engines .... hmmm (!?!)
(That's the same 'model' tranny as in our 2.0 FE's)
Color me 'intensely curious and puzzled'.