I think that the mothership hasn't been explored in the lore beyond the one mention so...
...no one knows?
If I had to guess though, I'd say the mothership is courtesy of an Anne McCaffrey fan or two at Riot. If you're looking to introduce a wide variety of different-themed champions, deliberately blurring the line between magic, advanced technology and psionic powers is a good way to let different kinds of powers, cultural influences and visual styles, etc. into your world.
Nothing like a "post-apocalyptic world once inhabitied by a post-singularity society now run overun with greedy primitives and no instruction manual" to get the creative juices flowing eh?
(Note: I would laugh my ass off if the "runes" on Runeterra just turn out to be the equivalent of computer chips harvested from a Jupiter Brain [look it up]. That would singlehandedly explain almost everything that has happened in the lore as well as every Champion's origins, powers and abilities but also render everything to do with the League and the League's "shadowly true purpose" utterly meaningless. All Runeterra would need then is "Ted from Geek squad" and not a heavily-armed army of gladiators culled from the most lethal beings across multiple dimensions.)