Idk if we can say they are on par with the goddesses. We still don't even know what exactly the secret stones are. Are they the Triforce fragmented more than usual? Something else entirely? It's all very unclear.
The Zonai tech is definitely the influence for the Sheikah Tech we see in Breath...
Yeah, it's a situation where I think it might be better for them to reboot the series to remove themselves from the timeline. I get the impression it's what they've tried doing with BotW and TotK anyway, whether others want to agree or not. It's not so far fetched to think Hylian civilization...
I would disagree that they've only been building up to it, they've already tried it before with the Oocca, for example.
I also don't think we can now look at a bunch of things from previous games and go, "oh, this was all related to the Zonai" I feel like it actually diminishes value in...
The Zelda series is not new to tribes being added out of the blue for one off games, incorperating new things to the lore, even if in the grand scheme none of it really matters. That's what we've gotten with the proper introduction of the Zonai in Tears of the Kingdom, but somehow this time...