As far as the subfloor, you have to do what you have to do. Sometimes it is easier to take up a bigger piece of existing floor. A larger piece of plywood will tend to be more stable. I have supported new plywood piece by sistering joists, using joist hangers to add cross-joists, and if necessary using a 2X6 on the flat between two joists. This is sometimes necessary as in your case adjacent to the wall where there is nothing else to support the subfloor. I support this with Simpson corner angles brackets under. Also select a really good piece of dry 2 by with minimal crown. If any crown noticeable, put the crown side DOWN. You can fill this with floor patch. You can not smooth out an upraise crown.
There are drill bits to auger out a fitting. They are very expensive. You might get a plumber to do it. But, since you have a lot of access, you can try to make vertical slices in the fitting with a saw blade held in hand, then try to pop out the pieces. This will usually work with ABS (black) but not PVC ( white )
The new flange should sit flat on top of finished floor. If you set if flush with tile, you will need to use an extension flange to bring the height up. This is done all the time in remodels where changing the flange is impractical.