The reason is said jenova dies in the safer battle is that

1. all of the battles against sephiroth before that were strange mutations with tenticals or wings ect.. while in the battle after that he is on his own, there is no presence of jenova with him but he is still determined to persue the twisted dream given to him by jenova

2. he is extreamly weak. you cannot lose even if you wait for him to attack you just counter attack and kill him instantly

eh i forgot about the false sephiroth actualy being jenova (but i did know, honest) but it does seem convenient that as soon as the other sephiroth appears he vanishes. but that could be because by the time you get back there he went to the reunion at the nothern crater.

but i dont think that the other "clones" are parts of jenova for the simple fact that they have tattos with numbers on them. more likly that they are experiment by hojo (like cloud and zack) on how older subjects react under exposure to jenova cells.