With the things that I do an M416 is, at times, very useful but it can also be a real pain. I don't have any substantial experience with a roof rack, but there are times when I wish I had one. During the course of a year I do a lot of field work, which is not expeditionary in nature but does involve some similar considerations. I don't have to carry extra water, fuel, etc. and seldom camp but I still lug around a pile of stuff. My work involves sampling for fish, mussels, turtles, cave life and in order to do this I have to carry seines, dipnets, minnow traps, SCUBA gear, wetsuits, cave equipement, plus coolers, clothing and other personal items. I don't take all of this on each trip but I often take enough so that packing it all in an FJ40 presents a challenge. Oh yeah, then there's the Hi-Lift, shovel, axe, tools, straps, chains, etc.
Depending upon the duration of the trip, the type of activity to be performed, and other considerations, I may decide to pull the M416. If I've spent all day snorkeling and diving in river the trailer comes in very handy as a receptacle to just dump the soggy wetsuit, tank, fins, and other gear. Same for caving. Nearly all of the caves I go in are wet and muddy, some extremely muddy, some require wetsuits. Often ropes and descending/ascending gear is needed. In cases like this having a trailer on hand is again very nice because all the wet, muddy polypropylene, cave suit (or wet suit), ropes, packs, and other gear can go into the trailer instead of the somewhat cleaner interior of the 40.
Plus I can simply load things into the trailer without regard to careful packing or having to lash it down, this would not be the case with a roof rack.
So in general, for my purposes, a trailer is very handy. Then there are the times when a trailer suddenly becomes almost more trouble than it's worth.