No, no, and no. Go back and reread, this time reading every word.
Attachment 70870
It is NOT the case that there are only a thousand universes total in existence, vs the millions that used to exist. As Sue's narration states, they didn't just
RESTORE the old multiverse, but chose to add their own creations to it - meaning that they DID in fact restore what used to be there basically as it was before they proceeded to
ADD their own special gravy to it. The thousand universes are
additional ones above and beyond what used to exist, got destroyed or crunched into Battleworld, and which Owen, Franklin, et al have now restored.
As far as natural universes in existence, it depends on your definition of natural... as well as on the origins of the previous multiverse. If the 7th universe had a creator or creators, even the One Above All, the Fulcrum, Celestials, previous version of Eternity, or whatever, would that be any more or less natural? Regardless of distinctions between artificial/created/natural, though, it seems clear that Entropy is an embodiment of the abstract principle for which she is named... and manufactured as well as naturally occurring entities are all subject to entropy and eventual destruction or heat death.
As to where Entropy came from, we've already seen in Ultimates already that the various cosmic embodiments have been recreated (albeit some in changed forms) as a consequence of the Richards family restoring the multiverse, including Eternity, Lord Order and Master Chaos, and so on. In this context, Entropy coming (back) into existence as a reaction to the restoration/creation of the multiverse seems to make a fair amount of sense. We also learned that this is far from the first time that this destruction and recreation of all of existence, including the whole multiverse once the First Firmament was fractured from one reality to many, with the current (ANAD, I guess) multiversal reality being the 8th. That makes the one we've been reading about all along prior to Last Days and Secret Wars the Seventh Cosmos, and the one that Galen of Taa (Galactus) came from the Sixth. We know from Ultimates that each iteration had its own Eternity-like embodiment, and presumably also a bunch of subsidiary abstract cosmic beings like Death, Entropy, Chaos, Order, etc. I'm not sure that their appearance in the Eighth Cosmos requires any more explanation than that.
But overall, the bottom line is that whatever new creations they've been engaged with, first the Future Foundation did in fact RESTORE the previous multiverse and all its realities very nearly as they existed prior to the Incursions and Secret Wars, making the Eighth Cosmos in some ways a continuation of the Seventh. Therefore, it doesn't make sense to regard the current MU and its denizens as any more 'fake' or 'artificial' than the predecessors whose lives they are continuing.... any more than we should regard the Captain Kirk and away team that appears on the planet's surface as fake copies of the versions destroyed on the transporter pad up on the Enterprise. For all intents and purposes, they are the same characters.