Just realised about the latest timeline: the Master sword problem from WW-TP is still present.
New thinking: maybe 3rd ganon is born between OoT and LttP, while 2nd ganon is in the sacred realm. I'm thinking Demise's curse didn't expand to other realms, so it didn't register any ganon in the light world during the gap between OoT-LttP. This means the curse would cause a new ganon to be born. This ganon attacks hyrule, but is somehow stopped by the castle guards or whatever. He's sent off to be executed, but ends up in the twilight realm.
New timeline:
SS-1st Ganon born-LoZ(1st Ganon dies)/AoL-MC-OoT(2nd Ganon)-3rd Ganon born-TP(3rd Ganon dies)-LttP(2nd Ganon)-OoX(2nd Ganon)/LA-WW(2nd Ganon dies)/PH-(ST any time after)-flood recedes-FS/FSA(4th Ganon)
There's still the twinrova issue, but until i find a better solution, i think she has a natural resurrection of sorts ('i'll come back to haunt you')