But the side effect of apple giving billions of dollars to these patent holders will just cause a gold rush to create similar patents.

Not really. Since there is no guarantee the same thing will happen with any other given patent. It's not like each patent has a great value. The ones which affect the critical markets are important. But trolls already push for making such patents to extort money so it doesn't really change the incentive for making more of them. Was there any higher patent rush after Google bought On2?

Does it benefit Apple? Is the lifetime cost of H264 patent licensing more than the cost to buy out all the patents?

I think it does - it creates interoperability for video on the Web. It benefits everyone including Apple. But they don't think in such terms or pretend that its not relevant. And anyway - they should profit from creating technology, and not from sitting on the pile of patents. But Apple is Apple.