@greenDarkness, 5th anniv eggs do not use method 2. They have a specific algorithm called DCEF (where a standard event is BACD). And shiny pichu eggs use an algorithm similar to berry glitch zigzagoons and it is DEFG (where berry glitch zigzagoon is BCDE). There are no fateful encounter flags for RS events. According to @ajxpk's research, these are the situations for the obedience flag:
- All Mews
- All Deoxys
- Egg Pokemon from Wondercards (PCNY WISH, PokePark 2004, PokePark 2005)
- Lugia/Ho-Oh from Navel Rock (EFRLG)
- Latios/Latias from Southern Island in Emerald
In addition to the anti-hack mechanism, I believe they did it because pokemon are from later games, when traded to Ruby/Sapphire might have issues without the flag.
Edit: I do not recommend creating 5th anniv eggs since the algorithm is complicated. The first 2 RNG calls are used to determine the species and move by doing a table lookup and some complicated nonsense. PKHex does not detect this properly, so you will get false positives.
I also do not recommend making BACD PokePark 2005 eggs (DS Download Play Distribution), since it most likely has some complicated species determination also that we do not know.