Horror Kid
Bob-omb
I suppose that it could be breaking the barrier, but to me it just seemed like it was spreading the monsters.
I really don't think that it was because of totk, nintendo tries to have a zelda game of sorts most years and skyward sword was the only major 3d zelda without a HD release.
Additionally, even if the islands are skyloft, I severely doubt the A.Rs have anything to do with them, the use Blue energy (perhaps derived from Nayru), are somewhat sentient, use completely different designs and styling compared to traditional zonai bots, and are only found in the Lanayru region, not Faron where the zonai seem to hail from. (Also the A.Rs are all dead and gone and Zonai architecture doesn't exist during Skyward Sword, so its difficult to know how they would have appeared over time)
But the ancient robots were sent to the Lanayru region to mine timeshift stones, I think. They do not need to be located in Faron as well necesseraly, I think.
Mining is also a very prominent theme in TotK, but that might be reaching. The different artstyle is obvious but that's just Zelda games.
But yeah, skyloft not showing any Zonai tech in Skyward Sword might be the biggest problem. Don't really know where I would place the Zonai otherwise though.