This also was confusing for me. The pop-up help for Output Format says "The project output format is what is used as canvas on the viewers."
This appears to not be an accurate statement. The viewer canvas seems to show whatever format is input to it, not necessarily the project output format.
I am new to Natron, but I am assuming that somewhere in the processing graph, it is the responsibility of the user to ensure that the images are explicitly reformatted to the project dimensions by scaling, cropping, etc.. In other words, Natron will not automatically resize or crop your pipeline to fit the output format. Is this correct?