I have seen a SOHC 2.5L Subaru engine with internal head gasket leak, after a warranty head gasket replacement. (Leaking coolant into the cylinders)
So it is not out of the question.
head gasket was replaced a year ago under warranty, then the chance of poor workmanship at that time is not out of the question.
I've lost track of which gasket was replaced, but if it was the passanger side there could be a relationship there with the #3 misfire.
I have never seen a 2.5L SOHC or DOHC head gasket that was compromized enough to cause low compression readings. A pressure gage on the radiator while cranking will give you more of an idication as to any compromize between the cylinder and water jacket, than will cylinder compression numbers. If you have documentation of compression numbers and they are all in spec and even, then you can assume that the cylinders, rings, and valve train are in "good" condition.
A pressure test of the cooling system, or a leak down test of each cylinder will reveal a lot more useful information as related to any possible internal coolant leakage into the cylinders. And the leak down test is bar none the best way to nail down even small combustion leaks into the cooling system. (well except maybe a gas analizer to sniff the radiator)