Let's see here. I've flipped, swam, got on top of my boat, cold hands, now I have to pull a line from my waist or my pouch, tie it on, and try to re-flip. Or, I've flipped, swam, got on top of my boat, pulled out the flip lines from the nice easy bag, and re-flip. Sure, you may only save a few minutes or maybe even seconds. But that matters big time in a serious situation. I will keep my lines attached to my boat, thank you.
To each their own. I don't think there is a "wrong" way. Do what you feel comfortable with.