I didn't make that up. I got that information from Zelda Wiki, which is a pretty reputable source.they arent "nice" in MM. you save one of the witches from near death...im pretty sure you would be nice to the person who saves your life too. there also was nothing anywhere in OoT saying that they were brainwashing Gerudo in OoT. you totally just made that up. keep in mind that kid Link never runs into koume or kotake which means that he doesnt know they are evil. youre thinking through your eyes, not Link's eyes. if link has never met them he doesnt know they are evil. if ganondorf is captured before they can do anything evil then they will run away before they get captured too. if the king of evil is easily captured do they stand a chance? they would flee and lay low. running a potion shop in a different dimension and not commiting acts of evil seems like a solid way to hide. the fact that they arent evil and the fact that you THINK they would be brainwashing Gerudo isnt good evidence. they have the same exact names, the same exact look and the same exact personalities (minus being evil). all of the signs point to them being the same characters.
now i would understand them being different characters if it was a game made years after OoT but its a direct sequel. too much confusion is caused if they arent the same characters and without any in game quotes or hints its best to assume they are the same witches. if they wanted them to be different characters all they had to do was give them different names. its not that hard to do... as i said earlier or in a different thread, either they are the same characters or the creators are EXTREMELY lazy and didnt change their names or even attempt to hint anything out of laziness and that doesnt sound like the Zelda crew to me.
Where are you getting this from, Ganondorf getting captured? Twilight Princess? MM was made long before TP, so I doubt there would be much relation in plot. Besides, TP takes place 100 years after OoT.
You do realize that Termina is an alternate dimension, right? There are tons of characters in MM that hold the same appearance and same name as they did in OoT, but are completely different characters. A good example is Anju and her family. They are obviously supposed to be the same people, but tons of facts don't add up (the members of the family are different in either game, for example.) So this means that they are alternate versions of the OoT characters.
You are right, there is no definite proof that they're not the same Twinrova. But at the same time, there is a lot suggesting it.