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Broadly speaking, automatics and CVTs are more lossy, if for no other reason than that they have hydraulic losses (torque converters, lubrication pumps, etc.). CVT belts have a certain amount of frictional loss as well.
Automatics typically have more economical gearing. My best guess is that people don't like to shift, so manuals typically have a much shorter top gear. Sometimes the difference can be dramatic.
In EPA testing, automatics almost always win. In the real world, manuals almost always beat older automatics (driver permitting). I'm not sure where things stand with autos made in the last 5 years.
I had a manual Fit for a while, and a friend had an automatic of the same year. His auto had a similar EPA rating (~30 combined). He regularly got low 30's, while my SO regularly clocked mid to high 40's tanks. The automatic had significantly taller gearing.
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I'll use a 2020 Civic as an example. Lower ratios are taller, and will result in better economy, all else equal:
Manual:
6th gear = 0.686
Final drive = 4.105
RPM @ 80mph = 3000
CVT:
Top ratio = 0.405
Final drive = 3.238
RPM @ 80mph = 1400
This is the normal Civic, not the EX or Sport or Si trim, which have shorter manual gearing.
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