User blog comment:Temporaryeditor78/bioware vindicated!/@comment-184.36.250.160-20120627222410/@comment-3450019-20121009133918

I believe this is the correct explanation. There's a bit of chatter with EDI where she says that the Reaper IFF's been fully integrated into her systems and that for all intents and purposes, the Reapers should mistake the Normandy for one of their own now.

Though that seems to be contradicted later when they a) pursue you from S&R systems after you 'ping' too many times, and b) take a few shots at the Normandy during the Rannoch barrage. But those might be explicable too; the S&R sensor pings might give Normandy away as not in fact being a Reaper, and at Rannoch the incoming shots might not actually have been aimed *at* the Normandy, but rather quarian ships where Normandy was just in the line of fire.