Bongiorno Stefano,
As you have noticed, the PV Elite lets you decide to disable or not the rigidity check, because of the large variety of applications for these flanges. For example, you wouldn't disable the rigidity calculation for an exchanger girth flange design, because you know, it will never seal if the flange is too thin, bolt spacing close to the uper limit. You would rather increase the thickness by 8-10% over the calculated thickness, sometimes even more. However, a non-standard flange for a piping connection, relative small diameter, you would rather disable the rigidity check to save a buck (again, only for non stamped vessels). Also, note that the flat face flanges are not governed by the Appx 2, hence you don't need the rigidity check.
As far as I know, the 2547 is still valid and you can use other means of ensuring the required flange rigidity.