Yes. Everything you extract from this file goes through to bst_source_orient.m or process_source_flat.m with the option 'rms'.
This is the norm value correct? So I am wondering what is the mathematical relationship between this norm value and the Hilbert magnitude (which will also be positive)?
Once you've computed the norm of the three signals, you can't go back to the original signals and compute the Hilbert transform.
The other way around: the signals are filter in various frequency bands, then the envelopes of the Hilbert transform are summed, you can't can't get back to a norm of the broadband signal.
So you can't establish a direct link between the two.
Am I misunderstanding your question?