Yep, makes perfect sense. Some trucks were worse than others. I have mine adjusted to shift at 5800rpm through all gears, no noise. However, my truck has zero lifter noise.
I would just stick with the stock tune then unless you look forward to some repairs.The noise is definitely only at high rpm, just before each shift. It also only is heard with the rev limited increased. If you run it without the tune and at the stock shift point, it will shift all day long without ever making a sound.