Does the fuel tank vent valve control the flow of air getting into and out of the charcoal canister not allow air into the fuel tank on a controlled basis? The fuel tank would siphon lock if it did not allow atmospheric air into the tank to displace the fuel consumed. Is the atmospheric air dehumidified at 100% somehow? The fuel used must be displaced by air due to the emissions systems and the positive fuel tank pressure that modern vehicles require for emissions requirements. So, there is the ability for humidity to accumulate in any fuel system. Granted more manufacturers have gone to plastic fuel cell's and that does in fact help somewhat with the accumulation of moisture, but it does still exist.
Mostly I would agree with you, but Fuel gets hot from, or any fluid gets warmed up by P.S.I., its a compression thing. No way around it. Return coolers if needed are the remedy, but alot of older motors don't really need it unless they are tuned and tweaked. Freezing lines on small "Brake Line" sized fuel lines directly to each individual injectors are always going to be a problem. Even the 7.3L Powerstroke with the oil and fuel galleries in the heads cause issues in the cold below 10/15F. The Powerstrokes you can plug in for 45 minutes and they will fire up due to the fuel and oil galleries in the heads and not externally exposed like the I.D.I. you describe.
Fungus in the tank on a diesel needs to be addressed well in advance, it is caused by moister, there are many. Easiest is Power Service Clear-Diesel Fuel & Tank Cleaner available at walmart. One of the better is, Power Service Bio Kleen Diesel Fuel Biocide, Nissan also makes a top notch allege biocide treatment available at class 8 truck truck parts house stores.