The Pandorica was created from a TARDIS
The TARDIS' siege mode looked a whole lot like a miniature Pandorica? It must have been Time Lord tech that the Silence was able to get their hands on... maybe even a repurposed TARDIS that somehow survived the Time War, now that we know that the Time Lords weren't annihilated (and since other TARDISes survived in "corpse" form in The House's alternate dimension, it's not a far stretch). Let's not sell short the technological capacities of the race who juggled entire planets, stuffed them inside a rip in the fabric of reality, and meant to use them to wipe out rest of the omniverse.This was the Boneless' second scheme.
They were actually native to the first dimension. At some point they successfully managed to dissect and analyze two-dimension beings, before successfully gaining width along with depth and inhabiting the second dimension. They won the first time around, and after learning depth existed the events of "Flatline" began. Had they won in this episode, they would've tried to hijack the fourth dimension of time and continued until there's nothing higher to reach.