Ra protects all of them in her own way (you'll see by the end of the season), but you also need to keep in mind that her top priority is to protect *Egypt* itself, over anything else, which is the reason why she does stuff and even lets certain "stuff" happen (my guess is she let it all happen because she knew Seth would be the only one to ever beat Osiris at his own game).
Same. You can trust Ra loves Seth and definitely prefers him over Osiris, but she will still meet out punishment as she is equally unhappy at the way both Osiris and Seth mistreated Egypt, even if she had always planned for Seth to get rid of Osiris for her (from the minute Osiris secretly used his position as king of Egypt to turn Egypt into a desert, out of his own selfish wish to have Seth closer to himself, and uncaring if the humans started starving as a consequence of no longer having enough fertile soil to grow food for themselves...).
Spoilers (not really though but reading Ennead on tappy which is ahead of mangago)
Ra is such a snake... It's like sometimes I love her and then others she makes me want to slap her. She going to make Seth speak on his rape infront of all the Gods? Is it because she wants to corner him into doing her bidding? Does she loathe him and want to embarrass him or is she doing it to name Osiris the real culprit in front of the Ennead? I also don't like how she is trying to absolve Nepthys of responsibility but at the same time I get what she trying to say even if it's just deflection.