Here is what we as players know about auto puffy ack, be it over CV, strats, or HQ. Once you enter in range of the guns, a box forms around your plane. It is within that box that the puffy ack is going to randomly strike. I believe it is safe to say that the more guns you're in range of the more puffy ack you'll be targeted by. I'm not sure if the size of that box changes with the size of the airplane, but I doubt it. Based on these few points here is all we need to remember while in puffy ack range:
A 109 is going to have a slightly smaller chance, in theory, to be hit by puffy ack than say a Lancaster(s). The Lancaster(s) take up more room in the "box". Not only id the 109 smaller but the it will be moving at higher speeds than the Lancaster(s) and will be out of the range of the guns faster thereby exposing themselves to puffy ack fire for less time. Less puffy ack = less chance of getting damaged. However, with both of those 2 major points being made remember that the Lancaster(s) can take a lot more damage compared to the 109 before it is adversely effected. So, pick your poison.
The only thing a plane can do to protect itself from auto puffy ack is to get out of range.
Each of the last 4 high alt (25k+) bomber missions I've been on over an enemy strat has resulted in damage to my bombers from puffy ack. Fuel tank and engine hits, mostly.