Sitting shouldn't be a problem for a diesel that's in reasonable good condition.
There are fuel additives that can be used to help eliminate water and reduce the risk of growing algae, even though it's not something frequently encountered with road vehicles. Additives can also be used to prevent fuel issues from cold weather.
The drawback to sitting for extended periods of time is that it can make small problems seem like bigger problems, for example:
A small leak in the fuel system make cause it to bleed down slowly and lose some prime. When sitting overnight it may not even be noticed, but over several weeks it can make the engine hard to start.
Or
Weak batteries may be fine for a couple days, but after weeks they may not be able to crank fast enough to fire the engine without a jump.
Regarding the idling, the issue isn't really hot starts as much as hot shut downs. You want to idle long enough to allow the egt's, oil temp, and turbo temp to drop. Unlike your average diesel pickup, most of the commercial trucks you see are hauling 50-80k lbs so after a long pull it can take several minutes or more for temps to drop to acceptable levels that you won't cook the oil sitting in the turbo.
If your stopping to take a leak and get a fresh coffee, it's probably faster for the driver and easier on the engine to let it run and equalize temps rather than waiting for it to reach a safe temp to shut down.
When stopping for the night with a commercial truck, unless you have an APU, the idling engine provide the HVAC to keep you comfortable and the electricity to power your electronics and fridge.
The only real hazard I can see from extended sitting it that there is more time for oil to drain back from bearings, etc. but typically letting it idle long enough to build oil pressure and idle smooth will get oil to all the critical surfaces while keeping loads at safe levels.
I'm curious though about the statement made earlier about maintenance that need to be done based on time and not use, and what maintenance would fall into that category?