I recently had some correspondence with a member about the use of Auto ISO in bird photography, especially for birds in flight. I was surprised that he assumed that when I post an image and provide exposure information in the Equipment Field such as 'Manual, spot metering, AI Servo AF with 4-pt expansion, f/7.1, 1/3200 sec, ISO 400' that I must be using Auto ISO. This is not the case, these days I never use Auto ISO except to demonstrate that it gives inconsistent exposure results that are no better than using the other semi-automatic shooting modes, aperture priority or shutter priority. I am sorry if any other members have been misled in this regard. The reason why Auto ISO is not recommended is because the metering varies depending upon the size of the bird in the frame and the tracking error. If the bird is small in the frame, a significant amount of the light used for metering the exposure will come from the background. If it is a light bird on a dark background, this will cause over-exposure of the bird, not to mention over-exposure of the bird if the metering wanders off onto the dark background. The converse is a dark bird on a light background and the same kind of exposure issues are the result. If the bird is big in the frame and dominates the exposure metering, it is likely that the bird will be underexposed. To get correct exposure in these situations, one needs to manually apply some exposure compensation. This is a kind of dog chasing its tail situation.
The correct way to shoot with manual exposure adjustment is to set the aperture (depth of field) and exposure time (to avoid movement blur) to suit the job at hand. Then manually adjust the ISO for correct exposure. I usually use spot metering and move the metering spot over the bird to the lightest part and adjust the ISO for correct exposure with reference to the camera's exposure meter visible in the viewfinder. For birds in flight I still use spot metering but set the correct exposure by metering off a target in the environment that has a similar tonal range to the bird I am expecting to fly past. For example, if I am on a pelagic trip, I usually meter off the first white bird that lands near the boat. Alternatively, I guess the required ISO and take a test shot of the first white bird that flies past. It does not take long to get the optimum exposure with the 'blinkies' just starting to show on the brightest white parts of the bird. With a little experience, one can accurately guess the right ISO for sunny and overcast conditions. If the ambient light changes during the session then one will need to make an ISO adjustment for the changing conditions but this is not a big deal. The advantage of full manual control of the exposure is that once set, and provided the ambient light does not change much, any white bird that flies past will be recorded with proper exposure irrespective of the distance to the bird, the size of the bird in the frame, and tracking errors. This is a much better way of getting proper exposure for flying birds than using Auto ISO.
I hope this clears up any misunderstandings regarding my use of manual shooting mode.