I noted one posting that raised my eyebrows - that freighters don't have cabin doors to separate them from the hold. I had never considered this before, and wonder what the reason (or at least the justification) is. To me, the default would seem to be to keep the crew isolated from the cargo unless there is a particular reason for them to go back.
Perhaps because that post is wrong. I can't speak for all Freighters out there, but EVERY Boeing produced freighter has a fire resistant door between the flight deck and the cargo compartment (freighter conversions are STC - so they may be different).
In the case of the 747-400F, there is a door between the upper deck and the main deck (fire resistant), and another door between the flight deck and the rest of the upper deck. Per the AFM and a placard on the main deck/upper deck door, it
must be closed for takeoff and landing, and in-flight except when main deck access is required (e.g. care and feeding of live cargo). The flight deck door may be left open in-flight (given there was no one else on the aircraft it wouldn't surprise me if they left it open to provide easier access to the galley and lav), but the upper deck door was almost certainly closed.
I've only skimmed the report, but it sounds like the cargo fire was almost directly under the upper deck, and it's intensity quickly compromised the smoke/fire barrier between the main deck and upper deck. The smoke problem in the flight deck was then compounded by the miss-fortune of having Pack 1 drop (for those who may not know - standard procedure on a 747F for main deck fire is to depressurize the airplane to rob the fire of oxygen, while the flight crew uses supplemental oxygen, then use Pack 1 to supply air to the upper deck to keep it at a higher pressure to prevent smoke entering).
Unless someone is proposing that the main deck be lined with several tons of steel fire barriers (and the usable payload be reduced to ping pong balls and down pillows), the only way to have prevented an event of this type is to ban significant quantities of self oxidizing cargo.