[Mithadan]

I did not mean to imply that Orcs and Trolls were "created" by Morgoth, though Tolkien wavers on this point, both in Letters and, to a lesser extent, in Morgoth's Ring. In particular, Tolkien debated whether Trolls were a creation of Morgoth, though he appears to lean towards the view that if a being can speak and make choices of his or her own, the implication is that they have "souls" and would therefore derive their existence from the "thinking peoples," Elves, Men, Dwarves or Ents. Of course, Treebeard says that Trolls were made in counterfeit of Ents. Presumably, he would know if numbers of his race had been taken by Morgoth. I do note that while the three Trolls in The Hobbit can speak, the Trolls in LoTR do not. This could be the subject of a separate thread.

Yes, Elves, Men, Dwarves and Ents entered into Arda after it had been marred by Morgoth, both from the Music as well as from his direct intervention into the world's development (which, as a matter of strict construction if one is so inclined, derived from the Music). Yes they were made of the stuff of Arda and were sustained by it. But I do not think that they were, ab initio, fundamentally corrupted as their essence and nature were derived solely from the thought of Eru. Certainly once they arrived they were susceptible to being corrupted, both in mind and in form.

Yes, because they were made of the stuff of Arda Marred, they were less at the time of their creation than they would otherwise have been. The Athrabeth speaks to this, at least in the form of speculation. Finrod seemingly rejects the notion that Morgoth could have corrupted the nature of Men either at the time of their creation or later so that they became mortal and Andreth, who was wise for a Man but not in a position to "know", takes the opposite view. That such deeply divergent views are present within Tolkien's writings only serves to underscore the depth of his work.

Your interest in fitting Arda into the framework of science is intriguing and refreshing. Others have voiced similar views here over the years. Tolkien certainly thought of the potential disconnect between modern scientific views and his subcreated world, considering whether it could be explained by tales of the Elder Ages being the imperfect interpretation by the silly Men of Westernesse, who lacked to knowledge to distinguish between myth and reality, of Elvish stories. I never liked this way of looking at things. In my view, Tolkien generally thought of Arda as being Earth, subject to the rules of physics and science but with added rules that either faded or disappeared with the departure of the Elves and the distancing of the Valar from the world of Men.