There is at least some amount of oil leftover in the heads for sure. Pull the Valve cover and you will see the puddles.

However, none of this would cause a high reading on the dipstick or change the oil pan's capacity. That's where the dipstick is reading. A motor could have sludge or a dent in the pan causing oil to pool and not drain. I've seen both,

What the manual says is irrelevant really. Who knows what number they are using. Maybe they are accounting for oil in the filter after the motor has been run plus the pan capacity, I don't know. It doesn't matter. This is why it is good practice to check the oil level after you have changed the oil and run the vehicle. And periodically check it thereafter.

What's the stick reads is the only concern. I have never used a manual to determine the appropriate oil capacity while performing an oil change.