Let's not mix appples and oranges. There is Manual Mode on the camera and Manual Mode on the flash.
When the camera is in Manual Mode and the flash is on ETTL, you must set the exposure for the ambient light on the camera and the flash will expose the subject. The camera settings do not affect the flash, unless you reduce the flash's ability to travel by choosing too small an aperture. (Distance =GN/ f stop)
When the camera is on Manual and the flash is on Manual, you have to set the settings on the camera and flash. You set the flash by using a flash meter.
You can have the camera on P and the flash on Manual. The camera sets the ambient exposure and you control the flash.
You can have the camera on P and the Flash on ETTL.
The camera meter you see in the viewfinder is not affected by flash at all.
Flash control and camera control are totally independent when the camera is in Tv, Av, and M, except the camera won't allow shutter speeds in excess of the X speed(sync) unless you are in FP Flash Mode.
In P Mode, flash output is automatically reduced when ambient lighting is high.
It helps to consider flash pictures as two exposures combined-the flash and the ambient light. You have to consider how each exposure will be rendered. You can choose to control one and have the other done for you, or do both on your own, or none on your own. (P+ETTL)
My own preference when using a single flash, is to have the camera on Manual and the flash on ETTL. That gives me the ability to determine how I want my background to look by regulating how much ambient light is recorded. If There is mixed lighting I can go to 1/250 and eliminate most of the ambient light, or if there is a nice sunset, I can meter to capture it in the background and use the flash to light the subject.