In my non-professional view, you have the right idea. There are ways to remove a flange with special cutters, but where you have the access, cut and paste is a lot simpler. A few things to remember are if you have a 3" drain, you need a flange that fits on the outside of the pipe, not inside. The problem using an inside fitting flange is that this cuts the inside diameter down considerable and can cause a clogging problem. Just 'cause they make the inside fitting flanges doesn't mean they are OK. If your drain is 4", either inside or outside fits are OK. Flanges should have a metal ring not plastic. Flanges are intended to rest on top of the finished floor and be screwed clear through and into the sub floor. I like to use #12 stainless steel screws, (Yeah, SS is probably overkill, but a few cents at this point is worth it to me) A 12" rough-in measured from the finished wall (not base molding) to the center of the flange ( where the flange bolts are located) is standard in the industry. Toilets for 10" and 14" rough-ins are available in limited selection of style. Note: There is nothing wrong with a 3" sewer drain. This answer may be like telling you how to build a watch when you just asked for the time, but maybe it can save you from some common errors folks make.