The timing doesn't even matter ... the writers are still stuck with the choice of making the starchild right (in which case Anromeda needs it's own anti-AI space magic to be in place) or making him wrong (turning the ME3 ending into a bad horror movie with no deeper meaning even for people who want to look for it).
His taint will affect the story telling.
Well that leaves the possibility of a devastating war, long ago, between synthetics and organics, leaving a remnant (synthetic) and a few organic races (Khet,etc) still clinging to survival in Andromeda. Proving the Catalyst's prediction right. Into this devastation the Milkway Ark Posse ride in, having left before the Reaper invasion (well at least before the crucible energy is fired, so the ending ramifications are unknown to the travelers) to take whats left from the ruins and create a new home for humanity (and Asarinity,Kroganity etc) in Andromeda...
Mmmm on further reflection BW might start MEA a long time after ME3. Then the ending states become irelevant as everything merges into a tech singularity anyway, and the Reapers are all gone..because of some vague reason the details of which have been lost in time. Then the bright and shiny new galactic civilisation created after ME3, having run out places to poke their noses into in the milkyway, need more room or whatever so travel to Andromeda...
Or MEA starts, like before sometime after the events of ME3 but not the far future. The player then imputs their prefered conclusions to the various plot points and the ending state of ME3 . This determines vague references throughout the game about the state of the Milkyway when they left it...
Or I am now getting a headache just thinking about the possibilities.. But my gut is telling me that BW will want to make sure that the Catalyst is proven right thoughout the Universe.. Now I think I'll load up ME3 again just to shoot him in the face some more times...