It really doesn't matter what you set the stack size too. If you set the stack size to 16, it costs Yx16 air pressure to move the stack into the machine. If you make the stack size 64, it costs Yx64. The reason it seems to work better is because Yx16 is a much smaller number than Yx64. So it takes less time for the machine to build/replace the lost pressure, like you said. Personally, I just use a hopper and 4 speed upgrades on the Input door. It's very very fast. I can get 5 stacks of 64 items into the machine in about 2 mins or so. Just drop the 5 stacks in, run around getting water or harvesting crops, come back, it's all done.
This is the most infuriating thing ever. I really hope a solution can be found for this. Since it seems unlikely that a solution will be found, can you use SFM to turn the spawner on/off? That's the biggest issue for me. I have a signal bus set up with a switch that lets me turn the auto-spawner on and off (like Landstyder used, it's awesome), but sometimes the lever connector gets blown off the wall by the creeper seeds (along with some conveyor belts). SOOOOOO frustrating! hehe