Rough in is placement of plumbing before floors and walls are completed. After walls and floors are completed we return to "finish" the plumbing by connecting to the rough in plumbing.

A toilet flange has notches and slots that are used to anchor the t bolts that anchor the toilet. The flange is orientated to be square to the wall. If you want to change it to sit at an angle the plumbing under the floor will need to be moved and a new flange installed so that the notches are at an angle.

Edit: I am saying the same as waderson85 is saying. Just in different terms.