I have never heard of overheating throwing a CE light. However, being low on oil definitely will.
I have a feeling you will end up with a blown headgasket, but that's just a hunch. The work on the car likely is related to the problem. I gather you had to have valves replaced because some object impacted the timing belt and this resulted in the pistons hitting the valves. When an engine has been through that kind of trauma there is no gaurantee that it will run right ever again. It probably will, if fixed competently, but it is not gauranteed.
Your warranty is void unless the repair shop was an authorized Subaru repair facility. The shop will say it's Subaru's problem, Subaru will say its the shop's fault. You can go to arbitration but you will lose. Trust me on this one, I had two friends in college who worked at the call center for a major Detroit automaker and this very situation (independent shop does work, then a problem happens) came up again and again.
When this happens again (it will), DO NOT remove the radiator cap when the engine is hot. A radiator cap can explode off with enough force to kill you if it hits your nose. Then DO NOT pour cold water in! That is a really good way to get warped heads.
I would get yourself ready emotionally to total your RS with your insurer. Sorry this had to be your first post, this is a pretty bad situation!