The handbook has maybe not taken schedule 14 into account. In the earlier part of the act, Section 254, there's "meaning of 'house in multiple occupation'" and this says a building meets the test (i.e. IS a HMO) if: the living accommodation is occupied by persons who do not form a single household. There is a definition of household which is as you would expect really. i.e. A normal family home, someone living with a partner, family with adopted kids etc etc etc. That is probably what the FSO's information is reference to, ask him to check schedule 14 and then get back to you regarding your new circumstances.
I would say you are in the clear, but look carefully in the housing act, as that is the true definition. ("A bloke on firenet says so" is not a good defense.!
The problem is, (IMO of course) despite technically 'getting away with it' that house you are talking about IS a house that is in multiple occupation, at your own admission really. I think the whole '2 households' thing was put in to stop people getting away with having HMO's and getting out of having to make the building up to a standard by using single rent books and 'clubs' and other tricks.
I would expect that if someone rented a house with a friend that is ok, but if you look at it from a common sense view, (i.e. Ignore the legislations definitions etc) what is happening in yours is basically a HMO that is not fully occupied, so check carefully.
Doing my part as an FSO I would rather be telling you to put those fire doors on to make the premises safer. (And get AFD, sprinklers, plasterboard everything, risk assessments etc etc etc)