What I meant by the metaphysical foundations of science is that there are many assumptions that are outright kufr that are necessary to do science. It has been said that you need to do a lot of metaphysics to get to a point where you don't need metaphysics, and even now philosophers can't figure out a proper materialist metaphysic. Science on the whole just ignores the problem since their concern is industrial production, not truth.
Science lies upon the assumptions that 'inert matter' exists as such, that you can determine by repetition 'universal laws' (see hume's problem of induction), that the universe if a closed system in which all causes and effects are material or produced by matter, and that all processes can be ultimately reduced to quantities, mathematical formulae. These all tend to drive one towards atheism. Reduction to quantity strips all objects of any qualitative properties, in fact science tends to pretend like qualities dont even exist or some how are produced by 'inert matter' which is a direct contradction, this strips objects of any 'essence' and makes the world appear as just a disparate, indefinite mass of quantifiable objects, nothing more.
Science, as such, lacks any explanatory value. This is because of its mechanistic and reductionist (to pure quantity) character. It can only describe or represent, it cant explain anything, that why there is something rather than nothing. So it is useless, even though the scientists vehemently defend it by the mentioning of the mass industrial applications of their science, which I might add, if these were absent, no one would care at all about their science.
So my question is why? Why would one want muslims to do science or to islamise it? The only reason could be to emulate the mass industrial production of the kuffar, since this is all science is useful for; creating vast amounts of soulless, useless plastic junk, and enabling this mass consumerist society to continue its pathetic existence. If muslims follow the kuffar, down this lizards hole so to speak, muslims will end up like the kuffar; materialistic, greedy, driven by desires and wants for material goods, mindlessly consuming and godless. So if we consider these masses of useless material goods as not worth having, there is no benefit in science at all.
Muslims have their own physical theories, though somewhat out of date, and if we were to use our own metaphysics as a starting point, any such natural sciences would be of a vastly different character, and we probably would not be able to match the kuffar in terms of industrial production.
Regardless, I believe their system will not last. Matter has the fundamental tendency to create disunity, chaos. This was a basic assertion about 'matter' made by the ancient Greeks, Aristotle included. We can see this easily in the materialistic societies of the west. There is no transcendent principle to unify their people, only a mass of desires and wants exist, they are only prevented from killing eachother en masse due to their belief that doing so would prevent them from satisfying their wants. This is an illusory stability, and the only thing stopping this mass chaos and slaughter from happening is the current relative level of prosperity.
It is evident that slowly the amount of 'chaos' present in the society is increasing, which eventually will lead to a dissolution of that society. Do not be fooled by their riches and technology, it is an illusion, it will one day be gone, since it is only predicated on cheap oil, once any prosperity disappears these westerners will complete their return to utter barbarism, murdering and raping eachother over their precious 'inert matter'.