I own a 2009 Raleigh Sojourn, so I can comment on that, but I am not familiar with the Fuji. I use the Sojourn for commuting, touring, and general cargo hauling with a trailer. The tours I have done with it have involved a lot of dirt roads, which it handles really well.
As to each point: the gearing is high, but I swapped the small (30t) chainring for a 24t, and that caused no problems with shifting.
The 2009 model does come with 32 spoke wheels and a brand of hub I had never heard of, so I had a new wheelset (36 spokes, A719, XT) built by the shop where I bought it. I did use the stock wheels for about a month of commuting, and didn't have any problems with them; depending on how you ride, you might not need to get different wheels. I kind of like having an extra wheelset for my primary commuting bike anyway, just in case.
The disc brakes are nice in bad weather and when pulling a heavy trailer, but are kind of a pain, because they seem to go through pads about twice as fast as rim brakes I have used, and the pads are more expensive. It is also really hard to estimate pad wear without removing the pads from the calipers.
There is toe overlap, but that is only a problem at low speeds. A related issue is that the third water bottle mount on the underside of the down tube is too close to the wheel for a bottle. I currently have my frame pump there.
It is a really heavy bike, and handles very well with panniers. I actually think it handles better with 30 lbs of gear than unloaded, provided you get the weight distribution right. You definitely want to put as much of your load as possible on the front wheel.
Another somewhat unusual feature of the Sojourn are the handlebars, which flare out a lot. I like them now, but it did take a bit of getting used to. If you are the dodge-though-city-traffic type, you won't want those bars, since they end up being about 6-8cm wider than regular drops.
Overall, I am happy with the Sojourn as a general purpose utility bike, but would get something with rim brakes if it were a dedicated touring bike.