CTR- Sole Proprietorships

In completing a CTR on a sole proprietorship should we follow the instructions on the 104 or the ruling we came across sited as FIN-2006-R003? The ruling and Q & A says to report two Sec. A's for a sole proprietorship. Could the ruling be addressing another form of organization. My understanding is that a sole proprietorship is just that. The ruling also says that the "mulitple persons" box in Item 1 should be checked.

There are previous threads on this topic, and yes it makes no sense given the instructions and other info concenring seperate legal entities (contract law).
BUT - FinCEN wants to see the DBA as a seperate person from the real person = multiple persons = with a sec A for the person and a sec A for the DBA.

I also understand that you complete the CTR this way for BOTH cash ins as well as cash outs / withdrawals conducted by the owner of a DBA.