My question is, how do we know when it's meant to be connected timelines and when it's a simple easter egg? Sometimes the easter eggs can mess with things too.You're correct that BotW has stuff from all 3 timelines, making it difficult to place. However, unifying all 3 timelines is impossible. The AT and CT timelines run concurrently to each other.The DT on the other hand doesn't since it's kind of a "what if" scenario. If Link is defeated in the battle with Ganon, then Zelda doesn't send Link back- no split.
"There is some evidence for this timeline. First, there are some locations that are seen only in the failed hero timeline. Spectacle Rock, a particular rock formation that looks like a pair of spectacles, is one of those locations (if you want to see it, the Gerudo Desert Tower is on one spectacle, and Vah Naboris rests on the other spectacle after completing it)."
Well Wind Waker does have Spectacle Island.