About saving the PS as absolute and relative in the file format : yes its possible, but...
I don't think it should be done. For a simple reason. The decision of using a PS as relative or absolute node will come down to artistic and practical questions.
You do have a valid point, but also imagine this : i've just built a PS in the editor, and save it as an absolute PS.
I load it in the Scenegraph, and test it out. It doesn't look so hot, so i decide i want to us it as a relative one.
If its saved in the file, that means I'll have to change it in the editor and save it again.
Where as in the code i just change from an absolute node to a relative one.
I don't think that the PS file should have details that are concerned about now their are used in a scenegraph.
In a practical sense, an engine should script how things are done : like a script for when a player shoots a gun , and it could be written in groovy saying that it should play this sound, and create a moving node with this 3D model , and also this PS in absolute mode, etc.
If you want to change the effect, just change the script, change from and absolute to a relative node, change the 3d model, etc.
With that said, I would like to know the opinion of other ppl about this issue. It's not written in stone, it's my point of view. If needed, I'll make the change to the API.
What about:
ParticleSystem ps = ParticleSystemFactory.loadAbsolute( bla, sceneBranch );
ParticleSystem ps = ParticleSystemFactory.loadRelative( bla, sceneBranch );
or
ParticleSystem ps = ParticleSystemFactory.load( bla, sceneBranch, true );
where the third argument specifies wether you want it in an absolute or relative node ?