SEISMIC MASS OUTSIDE THE DIAPHRAGM

There are many different ways to do seismic analysis. Among the ones I have used:
1) Equivalent Lateral Force procedure where I calculate my seismic forces and apply them to the structure manually (this is what I always did back in my design days).
2) Have RISA automatically calculate the equivalent lateral forces and apply them to each diaphragm level automatically. Which is what you're talking about. This only works for commercial building type structures that have clearly defined rigid diaphragms at each level.
3) Run a response spectra analysis.

Based on what you describe, option #1 sounds like what I would do if I were in your shoes. Or, I might use option #2, but supplement it with forces that I enter in manually for certain regions outside the diaphragms.

Note:
When you use option #2 in RISA-3D, the Load Combination that defines the seismic weight does NOT ignore the weight outside of the diaphragm. It just gets attributed to the nearest diaphragm level. If the model came over from RISAFloor, however, (where the diaphragms have defined boundaries) the load outside the diaphragms would get ignored.