Why? The Reapers having been to Andromeda doesn't mean they are there now. Andromeda wouldn't be touched by the events of Mass Effect 3.
The Reapers don't have to be there for there to nevertheless be significant consequences of the Reapers having been there in the past. At the very least, the ending of Mass Effect 3 has two options where Reaper knowledge about Andromeda could be exploited and Reaper tech utilised to travel there (Control and Synthesis), if they had ever visited before.
Not to mention if Reaper tech is just lying around Andromeda, either from this or previous cycles, the question of why isn't it being used to be in contact with the Milky Way will invariably be asked.
Which again opens the back door to making a canon ending, sorting out the consequences of the conclusion and all the other things Bioware clearly don't want to do. Easiest thing is to say "Reapers didn't go there, don't know anything about it, state of the Milky Way remains blissfully undisturbed by a canon ending being chosen".