Something makes no sense here. Southwest isn't for everyone, but they have figured out how to market their product, and they generally run an efficient service, done their own way.
And they seem very clear to me how to work their system. After all, they only book via the Web, so you have to go online to make a reservation. Right there they tell you how to handle the boarding process.
Sure, it's all a bit like lining up the cattle at the slaughterhouse, but they are pretty consistent, and follow their own procedures, unlike a lot of the Big Boys, who seem to make up new rules as they go through the day.