A little more digging...

The MT version is optimized for FE, and has lean-burn while the CVT does not. I had forgotten about this tidbit. So less fuel is burned--> lower exhaust temp--> longer catalytic heating--> more time out of emissions spec.

Also, the nonstoiciometric chemistry (too much oxygen) will result in relatively more N2 getting oxidized into NOx which is then aggravated by the cooler cat not scrubbing it out as well.

Also not helping:
The emissions test comes from the same data runs as the EPA FE testing. So for the MT, engine speed (and heating to a point) is at the mercy of the driver's shift habit. The CVT can keep it revving high to get up to temp more rapidly.