Middle C is MIDI note 60 by definition, which makes it the 5th octave C, or C4 if the first C is considered C0, which is traditional. This aligns with the piano which has middle C as the fourth C from the left which is C1 in MIDI terms.
Wikipedia
has a good page on this.
The C that the oscillator section sets is for the lowest C on the Rev2 keyboard, "note 0" if you will, which is in fact C2 by the standard definition. You will note that this makes middle C the second C from the left, which correctly sends MIDI note 60 with not octave shift.
The "middle C is C3" thing is common, but it does not align with either the scientific notation, the piano keyboard, or the MIDI numeric assignments. Best not to get too hung up on what number is used, since it is quite arbitrary.
So to answer your question quickly the Rev2 follows the "correct" definition of middle C as C4 and thus the lowest C on the physical keyboard is C2. You are setting this pitch with the oscillator section and all other keys add to it to get their respective pitches.