Harold Bloom is onto something when he describes how Paradise Lost reads today like science fiction. A lot of that is down to Milton's distinctively monist cosmology. For him, Heaven and Hell are not in separate parallel dimensions. He believed that if you get in a rocket and went past the solar system you will eventually hit the pearly gates. Angels are physical space-faring beings that eat food and excrete through their pores. God is an awesomely powerful alien. Imagine a benevolent Galactus sitting at the top of a giant mountain.
And what's interesting for the purposes of the poem (which the beginning makes clear is to explain the ways of God to men) is that our universe was not created ex nihilo. Rather, God fashions it using pre-existing materials. Philip Pullman may have fixated on these world-building elements because they indicate some limit on God's jurisdiction. The poem personifies Chaos as a grumpy grandpa that has to endure chunks of his realm being annexed by his more powerful neighbour, who builds Hell and then our world during the course of the narrative (and presumably Heaven as well before the action starts). So what if these materials exist independently of God? What if other awesomely powerful space aliens have built their own worlds?
Since Blake and the Romantics, it has been all too easy to get carried away with Satan and presume some subconscious subversion on Milton's part. On this re-read I did my best to stick to my university training and take Milton at his word, without being seduced by Straussian attempts to read between the lines. Fact is Milton was a deeply pious man trying to explain the problem of evil – an insoluble theological puzzle if ever there was one. What was important for Milton was that God freely chose to create – to share the universe with others. Likewise he left his creation enough freedom to dissent from his overwhelmingly obvious and necessary lordship. Although foreseeing the Fall, he allows it without interfering, preferring devotion that is freely chosen rather than mandated. The link with Milton's political liberalism comes through at the end, where he condemns religious persecution and a politicisation of religion that leads to citizens performing empty rites that do not express their internal convictions. The only royalty Milton submits to is God – kings are but men, and removable if necessary.
All that said, for me there remains an impression of God as a limited figure. He creates angels and then realises he needs the Son as a bridging device that will allow them to more closely identify with him (the Son will later fulfil a similar purpose for humanity). Needless to say, the plan backfires spectacularly. Adam and Eve are created in God's image, but they (like the rebel angels) are in some respects pre-fallen. Eve's pride leaves her open to temptation, like Satan. Milton is at pains to point out that Adam has all the knowledge he could possibly ask for and yet he still eats the forbidden fruit. God does not seem to have a grip on his creation – it spins away from him. His dark materials are wayward elements. There is still a little bit of Chaos in them. We're not too far away here from the atomistic 'mechanical' view of the universe that will become ever more prevalent during the Enlightenment.