This is a philosphical question. It is not generally recommended for the levain to be part of the autolyse process. And so I’d propose the following: Shorten the autolyse to 1 hour, you get 90% of the benefit of the 2 hour autolyse and you reduce the degradation chance of the levain.
How does that sound?
In terms of why not mixing the autolyse with the levain… The addition of the levain begins a different bread stage, fermentation and some oxidation. Purists will suggest you want to focus the autolyse on simply activating the enzymes locked in the flour. Can you still make a delicious loaf of bread if you mix the levain in with the autolyse, yes. But that might not always be the case – it will depend on the formula – specifically hydration, types of flour, temperature. It is a bigger factor with whole grains. I leave it to you.