Manual vs auto has lots to do with emissions.
The auto has full control over the transmission and the throttle. It can use them together to precisely control exactly how the fuel burns. The transmission is designed to work together with the engine to allow for shifts that minimize pollution.
In a manual car things get more unpredictable. The driver can push in the clutch and fully release the throttle at any time.
He also needs the engine to respond the the throttle quickly.
An engine that is tuned to respond to the throttle instantly will produce undesirable emissions (NOX, CO ect. ), so car makers reduce the speed of the opening/closing of the throttle to help limit pollution.
This reduced response shows up as rev-hang. In the CX-5 rev-hang only happens under specific conditions.
Car fully warmed up and shifts from 1st to 2nd and 2nd to 3rd under 4000RPM.
Either way, getting a manual transmission car to pass US emissions requires some effort from the manufacturer and with low sales many automakers choose not to put that effort in even-tough the manual transmission is available in may other markets.