i built both the armed and civilian version of the trawler many moons ago, and the Milford star was built as a reveiw model for one of the model; boat magazines of the day in the 1980/90's and i cant in the fogging of time remember it advogcating fitting the deck in that order.but as i say it was at least 30 years ago.
however my one best tip is to make sure you have the running gear, prop shaft, and motor bed and motor fitted before the deck goes on permanently.
Also as a help I made a waterproof hatch incoroporating either the fish hatches [civilian ] or the box mounting for the 4 pounder [armed trawler]on the fore deck to allow the placing of the propulsion motor batteries, as if you dont the possibilities of doing any maintenance is very limited, because the access under the main superstructure is very very limited indeed.