For exceptional loads railroads need exceptional cars. So-called heavy duty flat and well cars use additional wheels, lower decks, or even separable frames to distribute the weight and allow large and heavy loads to safely pass beneath tunnels and bridges. Like the cars, the open loads for heavy duty flatcars are often the most impressive thing in any train.
Kits for electrical generators, boilers and machinery are available. More adventurous modelers could build their own. One easy solution to this is to model a load protected by a tarp. Since these loads are rare and very distinctive, time and effort spent on projects like this are well worth it.
Close clearances mean special operating conditions. Some loads are so challenging they require their own train. Dedicated trains are expensive, but keep sensitive loads out of freight yards and prevent delays to regular trains. Some cars are so big they even require special handling when empty.
Extra idler cars are often added for increased braking power or to keep heavy locomotives and loads from simultaneously occupying light bridges. Trains move at reduced speed and on specific schedules. If the load is wide, meets with passing trains must be carefully planned. Even today, a caboose is usually included to accommodate railroad and shipper inspectors.
Since these cars are only needed for special moves, they must be stored someplace in between runs. Often, a large centrally located yard will have a dedicated track for storing special cars. If you model a yard like this, you can generate a lot of traffic for empty cars without ever modeling the loads themselves.