I believe bubble stacks are mainly visual. My reasoning is that stale water stacks to the top of my tubes while fresh water doesn't. My tubes don't hit any smoother with fresh water than with stale water even though it stacks twice as high which makes sense because its the same exact perc.
In engines and pc waterblocks water turbulence is much more effective at transferring heat to the cooling fluid than the rate of flow - not a direct comparison but close. Turbulence is what allows VXH products to pump out a seemingly never ending stream of hot air.
Diffusion creates turbulence in the water and vapor therefore improving heat transfer by allowing more water/vapor to come into contact with fresh, cool water/vapor. Only so much heat can be transferred to the same water, especially when its a minuscule amount like the water forming a bubble. The more fresh, cool water and vapor that come into contact each other the more efficient the heat transfer.
If bubble stacks make a difference it is without a doubt negligible because the water in that bubble can only do so much in the way of transferring heat.