It does not refer to any states being in rebellion. The text was worded very carefully. See #104.
Semantics. Are the 'people' the state, or is 'geography' the state?
But yes, for the purposes of not making the case for the states being in rebellion, and therefore providing a tacit admission that they are part of a recognized 'other' union, in this case 'The Confederacy', Lincoln worded the Proclamation correctly.