Well I have a few things to address...
First, it's pointless to distinguish between metaphysics and reality when talking about the possible existence of god(s). If God is a reality, then it is no longer metaphysical or 'beyond reality.' You cannot argue for the existence of a god and also claim that it is beyond the 'natural/physical world'/reality, it's a logical contradiction. Can't have it both ways.
Secondly, i agree with you Aj. God or the possible existence of God isn't incompatible with science. If god is a reality, then science, a methodological tool used to describe reality, can (hypothetically) describe god. Science follows the evidence, and if that's where the evidence leads, then so be it. Problem is, there's no evidence. Doesn't help that theists of all kinds make it especially impossible for us experiment on their god(s) by adding in a bunch of arbitrary restrictions (gee, i wonder why!).
In regards to religion, what is incompatible with science are the claims of religious texts. Now for the sake of the topic I'll restrict 'religions' to the major religions of the world. Whether it's Hinduism, Islam, Christianity, Judaism, Shinto or whatever, they all have something in common: creation stories/myths/w.e that are beyond doubt wrong. Now of course religious people can easily get around this by providing ad hoc arguments (a la re-interpretation) when confronted by scientific discoveries.
Another incompatibility: faith. Faith is irreconcilable with science, they are inherently contradictory. It doesn't matter if it's religious, political, or w/e faith, it's still irreconcilable. Faith, complete trust in unsubstantiated(without evidence) claims, cannot possibly be reconcilable with science, a methodology centered around empirical evidence. That isn't to say you can't believe in God/have faith and be a scientist; you can. The thing is, publishing scientists throw out their faith before they enter the lab - quote from some dude.
And that's where Newton comes in -
Nowhere in his laws of motions or universal law of gravitation does he describe his faith in his god. It's only when he reached the limitations of his equations that he decided to invoke a supernatural cause. Newton is a prime example (and a popular one too) of great thinkers invoking a "god of the gaps."