Why exactly, did Rachel call her son 'Yosef'?
Rashbam: For two reasons: Basically, because Hashem had gathered in (hidden) her shame, only then, he ought to have been called 'Asaf' - so she replaced the 'Alef' with a 'Yud Vav', to hint at the second child that she hoped to bear 1 (or prophesied that she would).
What made Rachel think that she would bear another son?
Seforno: She assumed that she was granted her first son on account of her first Hashtadlus (Refer to 30:22:1:2), and that she would be granted a second son on account of her second Hashtadlus.
Tosfos ha'Shalem (4): The son that was changed inside [Leah] to a girl, was in order that I can have two sons. 3
Tosfos ha'Shalem (3, citing R. Efrayim): She expected to be no less than her Shifchah.
Oznayim la'Torah: When she gave Bilhah to Yakov and declared "ve'Seiled al Birkai, promising to bring -up her son as her own, she knew that Hashem would repay her 'Midah Keneged Midah', and grant her a son. And she felt certain that, now that Bilhah had given birth to a second son, whom she would also raise on her knees, Hashem would repay her with a second son.
Which explains why she Davened for only one more son. However, the Yerushalmi in B'rachos, 5:5 extrapolates from the fact that she only requested a son and not sons, that she was incluyded among the first Nevi'im.
Perhaps she knew this through Ru'ach ha'Kodesh. Or, the Imahos (Yakov's wives) had gathered to pray for this (Bereishis Rabah Sof 72). Or, Rachel could have known that initially her own fetus was a girl (refer to 46:15:1:1; see also Tosfos ha'Shalem 22:2), and understood that Hashem switched the fetuses to enable her to have two sons (PF).
What are the implications of "ben Acher"?
Oznayim la'Torah: This was a hint that Binyamin would not be together with his brother Yosef, but would join Yehudah, whilst Yosef (Efrayim and Menasheh) was was the leader of the ten tribes.