You actually have two problems to deal with. The flange is supposed to set on top of the finished floor, not level with it, and the orientation of the flange bolts. One possible solution is to remove the flange completely and install a new on. Since you are dealing with a 4" drain, you can use a flange the inserts inside the drain pipe. While removing the old flange will be a PITA, the biggest problem will be anchoring the screws. There are a couple of ways this can be done, but here's what I'd do. I'd drill new holes around the flange so that the screws would be spaced between the old holes. For anchoring into concrete, I use a rotor hammer drill with a 5/16" SDS bit the will easily drill into concrete. Then 3/8" lead ferrels for the #12 SS screws. Basically after I drilled the new holes in the flange, I would orient the flange so the flange bolts were in the proper location, mark and drill one hole, put the ferrel in place and insert a screw. Then mark the rest of the hole sites, remove the flange, and drill the remaining holes, install the rest of the ferrells. Then install the flange, gluing it to the pipe then screwing the ring down. You might not have to drill the new holes in the flange is the new flange holes are already spaced differently from the old one, you just need to avoid the old holes unless they line up perfectly with the new flange. Hope this is not too confusing, but I have used this method to anchor may things to concrete with great success. It does help to have access to a rotary hammer drill, but they can be rented.