The distinction between civil and military was a little blurred, and I suppose mostly because they tended to transit via Eire and Portugal, neutral countries that would intern servicemen and military equipment that arrived there. Towards the end of the log, the registrations change from civil to military and the "Capt" pilot becomes "Flt/Lt", though the destinations stayed largely the same. The Anson ferries to Cairo didn't land in either neutral country, and went via Gibraltar, then the crews were ferried back in Dakotas.
I found a very interesting document
here which gives a lot of information on BOAC operations during this period.
What's very striking is the punishing schedules. Long day flights followed by lengthy night flying. May have been the reason why my grandfather didn't fly much after he left the RAF in 1946, I guess he'd had his fill of it. Sadly he died when I was quite young, suddenly of an aneurism, so I never got to talk to him and hear his stories. I inherited a heavy plastic fertiliser sack full of charts and books and mementoes, most of which have been lost over the years unfortunately.