When Padmé as Queen is looking out her palace window as the battle droids march up the streets of Theed, you could have create new off-screen dialogue of a guard or handmaiden regarding the switch or decoy.

Something like, “Hurry, your Highness, your decoy is ready.”
or
“Your decoy is in position. We need to disguise you quickly!”

When Obi-Wan calls her Your Highness during the briefing, maybe you could somehow re-implement Anakin’s reaction shots from her theatrical reveal. I guess this would be the first time Anakin would realize it in this version, but I don’t think it is hard to assume everyone else was informed offscreen, if they didn’t already know.