You don't build VC-25s on the -8 line. You take two completed -8s and retrofit them to be VC-25s using a process you kind of develop on the fly, since it's a one-off. That said, you still want access to -8 spare parts.
Metal fatigue is more a problem for aluminum than steel, but airframe construction uses exotic aluminum alloys that make that kind of a minor concern. The fatigue modes associated with carbon fiber composites are completely different.
If you have infinite budget, you can extend life indefinitely. The Air Force has a program to keep the B-52 airframe flying until the 2060s, making some of them 100 years old at their expected retirement. But with Air Force One, you don't want long repair cycles. There are two of them, but the longer and more expensive it is to repair them, the more it makes sense to just replace them after a while in order to support the mission.
Maintenance is not necessarily about metal fatigue. It's about dumb things like cable harnesses and connectors, hydraulic fittings, valves, switches, relays, sensors, etc. These are all supplied by subcontractors initially, but when the -200 goes out of service there's no more market for those parts and they stop being made. The subcontractors have moved on to new designs for those components that support the models still being flown. You can have replacement parts, but you have to make them yourself and verify their safety and function. That gets very expensive and time-consuming.