We native speakers confuse ourselves on this issue too. I recommend using 2 as it can mean only one thing. If the red apple is 3 cubic cm, then the green one is 9 cubic cm. I would interpret option 1 to mean "4 times as large" i.e. red = 3 cubic cm and green = 12 cubic cm. But sometimes, people mean 9 cubic cm - same as option 2.

I see what Michael is saying about interpreting option 1 to mean "4 times as large". However, I think that only a teacher who is dissecting this sentence would see it that way. I think in terms of every day speaking, native speakers would absolutely use either of these 2 sentences to mean the same thing.