Safe, perhaps. Not sure what is unsafe here.
And there is another way: just make the fields you don't want to be serialized (eg. those which are always computed, etc.) transient.

The problem phi.lho is that I was wondering if PApplet does any JNI call where it allocate native resource or is it somehow tied to the execution environment.

I can't say for sure, but RegistredMethods are here for libraries to be called automatically by Processing during the sketch run.

AFAIK, Processing doesn't do native calls (outside those made by Java itself) in regular sketches. It can do that with libraries like Serial, OpenGL, or perhaps Minim.