Correct, Ungoliant came from beyond Arda, but likely from somewhere else in Eä -- which in your words means she's came from somewhere in darkness of space outside the solar system. Shelob is her spawn, and Charlotte is her great-great-great-grandspawn. She's powerful enough that she is a Spirit, which is to say of the race of Ainur but fallen. I can't imagine how something like that could fit into the Sailor Moon universe. 
The origin of orcs is a plot hole, and one that JRR himself realized. He wants true creation of souls to only happen through the Flame Imperishable (read: Holy Spirit) held by Illúvatar alone. But I mean, come on, we need some good baddies for our story. And where do the fell creatures come from? Over his life he went across a lot of potential origin stories for the orcs, for which the corrupted Elves is only one. Possibly they're not really "alive" in the same sense, lacking the souls, similar to Manwë's Eagles. But then there's that whole scene where the orc commanders are talking to each other and they seem kind of sentient. Maybe men were bred in there later? Perhaps the orcs were automatons when first made by Morgoth, barely smarter than the average Russian conscript, then perfected later by Sauron? Perhaps youma are in somewhat of the same category. Speaking of which:
Open questions:
* What are the youma and where do they come from?
* For the seven great youma, are they people possessed by youma, or did they become youma, or are they only possessing people in the Seventh Age but were fully monsters in the Fourth Age?
The origin of orcs is a plot hole, and one that JRR himself realized. He wants true creation of souls to only happen through the Flame Imperishable (read: Holy Spirit) held by Illúvatar alone. But I mean, come on, we need some good baddies for our story. And where do the fell creatures come from? Over his life he went across a lot of potential origin stories for the orcs, for which the corrupted Elves is only one. Possibly they're not really "alive" in the same sense, lacking the souls, similar to Manwë's Eagles. But then there's that whole scene where the orc commanders are talking to each other and they seem kind of sentient. Maybe men were bred in there later? Perhaps the orcs were automatons when first made by Morgoth, barely smarter than the average Russian conscript, then perfected later by Sauron? Perhaps youma are in somewhat of the same category. Speaking of which:
Open questions:
* What are the youma and where do they come from?
* For the seven great youma, are they people possessed by youma, or did they become youma, or are they only possessing people in the Seventh Age but were fully monsters in the Fourth Age?
"Kitto daijoubu da yo." - Sakura Kinomoto