...by providing lore and context that never happened in two of the timelines?
Which two? I've found lore and context for all three. Admittedly, I have found the least for the adult timeline, and the most for the downfall timeline. The most obvious reference to this idea is the quest to find the bones of the three leviathans. Each is stated to have died under drastically different conditions, lining up with the three timelines.
The connections are there, however tenuous. So, including room for all three timelines when talking about Breath of the Wild just makes the discourse stronger, not weaker.
(as a side note, I don't know why my shrug emote was changed to a male symbol... I'm going to try to fix that.)