I think your software is making the intelligent choice in both cases. Don't hesitate to ask your vendor about how it came to make certain decisions or ask for the name of a long term user who may be able to give you some insight.
While questions regarding forms completion should fall to the IRS, FinCEN operates a Helpline which you can reach at (800) 949-2732.
Not that you asked for it, but you opened the door, so here's the relevant paragraph from the comment letter I filed on the request for reduction in the regulatory burden:
*Calls to the IRS Detroit Computing Center Hotline, 1-800-800-2877 should be answered or at least callers should receive the courtesy of having messages returned. I have had dozens of anecdotes offered by seminar attendees where they never received a response to the message they left. I have had the same experience. (I’ve had no reports of similar experiences with banks using the FinCEN 800 number. They have also answered or returned my calls promptly.) However, sometimes what a bank needs is simple information regarding form completion or assistance with a backfiling problem on CTRs; that is the Computing Center’s responsibility, not FinCEN’s.
So far, no results.