What if we are reading something wrong?
Do you mean what if the reader is reading something wrong despite the author's words outside the story?
My reason for wanting to do something other than my existing Roads of Time writeup is to simplify the opening and the assumptions the reader has to make going into the story. It should make the ancient letter discovered in the Vatican archives shorter and less convoluted. There are only so many things I want to ask the reader to accept as up front assumptions before the story even begins (e.g., Satan issues the challenge, God accepts, that changes the future sufficiently to deviate from the Bible, explain why didn't the Bible change to reflect the new timeline, etc.).
There's a lot to be said for the simplicity of "In an alternate universe...." It would allow me to do pretty much anything I want and leave the details of trying to explain things until later (over the course of the three books) and perhaps leave some of the details to the reader's imagination.
So:
In an alternate universe....
The ancient letter says discrepancies will be explained by the Lord.
Since I'm deferring explaining some things, I may not even need to mention an alternate universe outside the story. If it's important to the story, perhaps the characters can figure it out (or at least speculate correctly).
Voila!