You will have to rotate the flange so the bolts line up how you want. That either means a new flange or a new repair ring that will fit the current flange. You may also have to use a longer water line since it probably won't be lined up straight anymore.

The other comments about plumbing code are valid, but if it's your house you can pretty much do what you want. Just be prepared to put it back if you sell the house, or possibly take some flack regarding the inspections and other potential hassles. It's also possible that if there is a flood/leak or something and your insurance adjuster deems that it was "installed wrong" you could be looking at denial of coverage I guess.