Wait... three were killed? Woah, I gotta stop working on 100% and play through it again.
I suppose it would work better that way, but wouldn't that mean that there should have been are 9 sages in TP?
As for them not knowng about his ToP
Idea 1) he sages seem to be different just by the apprance of their form. They could just be uninformed, and wanted to eal Ganondorf in the Twilight Realm rather than the Sacred realm.
Idea 2) Perhaps they knew about it, but thought of it as an essential risk to further seperate Ganodorf from the Sacred Realm.
Idea 3) They forgot (couple hundred years)

just kdding
Idea 4) Ganondorf somehow escaped, and they had to subdue him ASAP.
It would depend what side of the split you put it on. If you put them both on the adult side, then Bong Bongo would have attacked.
Well, the way I picture it is that during OoT, people knew what was happening, and they recognized the heroes (Sages and Link), while in TP, they are pretty much oblivious, I bet they didn't even have a clue about the sages.
I may have to re read the interview, but I thought it only said TP hundred(s) years after OoT, TWW thouand(s) after OoT. Don't remember it mentioning the endings.
As for Termina, the would be HoT went there, and came back 3 days later. This was probably 3 days after Ganondorf was one of two things attacking or apprehended, depending on your views on the timeline
I kinda view MM as suspended on its own timeline, as it is seperate realm from Hyrule. Although it takes place after the child ending, I kinda think it should have a seperate section of the timeline.