William, I see the 5:4 ratio feature to have two practical benefits: (1) you can compose with it in-camera, and (2) the files will take up less space, meaning that one can store more images on a CF card. But in terms of getting the files to be cropped to 5:4 and having it look that way on a computer, I don't see any advantage of this. For instance, I use LR and if I want a certain aspect ratio crop applied to a group of images, I just create a preset for it, then apply it to all the images. Or, even better, I can apply the preset during the import process, so that it becomes fully automatic ...
I think there are advantages both ways. With the 5:4 camera feature, you can do it in-camera, but if you goof on the composition, the extra pixels are lost. Without the feature, you have to imagine the 5:4 ratio in-camera, but then you have more flexibility in cropping later.