I don't think it's and issue of a better way. Each has it's own purpose. If you plan on throwing another punch, then you need pull the fist back fast after it has done its job. This will allow you to throw a second punch.
You can leave the fist out with certain techniques so you can flow through or you can leave it out to flow into a different technique.
Two examples. Double Jab vs. Circular long fist punch
Long fist punches like this require that you punch all the way through. Trying to pull this punch back quickly will only cause injury to the person throwing it. Even when it lands, you want the force to continue. It's like swinging bat. Do you try to quickly pull the bat back once it makes contact or do you swing all the way through?
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Each punch has it's own requirements, so a person should be focused on "What is better for punching technique A? Leave it out there or pull it back? What is better for punching technique B?"