As for where the darkness came from if not the RoD, when the worlds were all joined together originally as one world, they were still surrounded by the Lanes Between, which is darkness. I think this was brought up somewhere on the last page. Perhaps the darkness from there seeped into the world (which at the time, people were unaware that in their world of light they were surrounded by darkness, since no perforations in the worlds had been made yet to let darkness through).
That seems unlikely because at that point in the worlds history the world was connected and one, it wouldn't have the Lanes or even Corridors since there was no need for such paths.
The Lanes and Corridors function as paths between the closed off worlds of today, in a world totally open and connected they'd have no purpose.
I guess it's possible that the RoD is just an extension of the world they couldn't restore, but I just don't see why when worlds are taken over my darkness they are sent to the RoD. If the RoD is just another normal part of the world that can't be restored, it would be plausible to assume that it's just like the RoL where there are worlds stuck down there that will always be there since it is just another part of the world (which is possible).
You have to remember the nature of worlds now and the nature of the single world then are different, what's the norm now wouldn't be exactly the same as then. (at least logically speaking)
As for why worlds sink into darkness that's something you'll have to ask nomura as it's not only worlds but hearts in general that sink into darkness.
Darkness seems to be the end game, for whatever reason when something disappears it sinks into darkness.
Though if I had to guess it's likely due to kingdom hearts presence within the dark realm. It's the source of all hearts so when something like a person or world loses that heart them going to the dark realm may just be them trying to return to their origin.
Of course if it's a heartless that taken a heart it makers perfect sense something is dragged into darkness, to have your heart taken or become a heartless is the same as sinking into it.
However, given how they've implied the whole "once you're taken over my darkness you're sent there" and darkness, while not bad, is heavily implied to be malevolent, it seems the RoD is more of a realm where worlds go if they "die" so-to-speak, couldn't think of a better term for that and that doesn't sound like a "part of the world."
Dont forget sleep, as Ansem says "darkness holds sleep" so it may also tie into that. When something "dies" in kh it's cause it's physical form has died while the heart goes somewhere.
And given were the lost hearts of worlds from kh1 ended, the realm of Sleep, it may very well be that sleep is the end game and things sink into darkness simply because that is where sleep is held.
It's all really an assumption game really and to me all assumptions seem plausible.
All that we know for sure is that darkness had to exist in some form or fashion since the universes inception else the xblade itself would be an impossibility.