Those hose is a insulator, metal tubing has the ability to disipate heat. There are problems that could happen with a hose like inner shell/liner could deteriate and fold over blocking flow from the inside, I doubt this would happen with ATF but I've seen it happen with other oils. Surely Mike has some more reasons also.
In my experience the more exposed hose you have on a pressure line the more chance something can happen. Rub through, heat insulation as you mentioned, heat from the outside touching the hose. I use hose only as a last resort. I would keep the hose as short as possible.