It's not a what-if. What if's aren't canon. It's just another timeline. I mean, that would make the original Zelda game, as well as every (non-CD-i) Zelda game up to OoT, non-canon if it were simply a what-if lol.
So, I'm pretty sure that would make the Golden Goddesses 6-8 universe level, depending on if we treat the Sacred World as a separate universe or not (we should, especially as the Silent Realm is debatably a beta version of the Sacred Realm). Worst case scenario, the Golden Goddesses creates two timelines: 2/3 of the Unified Timeline (as the split of the Child and Adult Timelines was created by an outside source and undoubtedly independent of the Goddesses) and the Downfall Timeline. Middle (but not most likely) scenario, the Golden Goddesses are six universe level, as there's the Light World, Lorule, and Termina in both, the Downfall Timeline and the Child/Adult Timeline, and we don't consider the Sacred Realm/World (For the record, they're the same thing. I just change it up to coincide with either the Light World or Silent Realm) a separate universe, or it being in the same timeline as the Light World. But again, Zen'ō's not Low 2-C there.
For the record, if you're thinking that having the Sacred Realm as a Low 2-C structure makes the Triforce, and therefore Link, Low 2-C, that wouldn't be the case. Even as someone who advocates for universal Triforce, the Triforce would only keep the physical side of the Sacred World intact, as a destroyed Sacred Realm still is able to be traveled to and isn't a void devoid of timespace.