John, B31.3 does include torsional stress in flexibility analysis, however, it does not intensify it.

Also, compressive stress would be required to be considered per para. 319.2.3(c) when it is significant. However, you will also have to realize you may need to check column buckling.

Use of 319.4.1 is problematic. Remember, though, that you as the designer are responsible for your judgement in the application of that paragraph. If the piping or nozzle fails, it is your responsibility, and you cannot point to that paragraph as blessing the system. It only gives you the latitude to exercise judgement and does not make the judgement for you.

I would consider it bad practice to rely on gasket flexibility. First, the gaskets are already compressed by the bolt up. Second, if the system thermal expansion is actually able to significantly compress them more (which it will not do until the system thermal load exceeds the bolting preload), it would likely result in a leaking flange joint when the system cools down.