I think I mostly understand it.
The "original" Miyuverse, before the revision caused by Illya's time travel, is one where Pandora's Box wasn't opened, and where Darius won. (I'm not sure if those two events are related or coincidental)
That Miyuverse was judged as a bad end and thrown into Pandora's Box, and presumably the Box inside it (that the giant Darius is reaching towards) recursively leads into the same bad end world.
Meanwhile, the Miyuverse revised by Illya's time travel is now the "real" Miyuverse. This is the world where Pandora opened the box with Illya's help, where Illya doesn't exist (or does she), and where Miyu defeated Darius.
This defeated Darius entered Pandora's Box and ended up in the bad end world, sitting next to his alternate timeline giant form.
And Illya is there too because I guess this is where she ended up after getting lost in time.
Which makes me wonder. When the box was spilling endless mud earlier, was it coming from the bad end world, which got covered with mud coming from Pandora's box, and it's mud and boxes all the way down? Or is it just a natural property of the Box to produce mud?