I don't have much experience with Fail Safe systems but I 'm sharing what I know.

In Siemens you can use S7-400H for a general continuos control and you can use the same CPU (which has the same MTBF[Mean Time Before Failure]) as Fail Safe CPU.
So, to the best of my knowledge the main issue is the MTBF and the self diagnostic capabilityof CPU.

In general purpose systems, it would be better to buy I/O modules with diagnostic capabilities but it is not a must to do so.
In SIS (Safety Instrumented System) all I/O modules are equipped with diagnostic features to detect any fault in module, individual channels or even the filed signal itself.
Even in digital modules, there are some specific tests performed by module at constant test intervals to make sure that there's nothing wrong.
Such tests can be open circuit test or short circuit tests or some other tests I don't know.
The Fail Safe I/O modules also support some special architectures (both module and channel levels) to comply with SIL2 or SIL3 requirements.

Also on the software side, there are pre-engineered blocks that you have to use and there are some restrictions.
So, you are not free as in general purpose PLCs.

Now, I would like to leave the MTBF and self diagnostics aside just to tell you that the whole story lies beneath TUV certificate.
the most important difference is that the Fail Safe PLC is a third party certified PLC which means that this system has the appropriate MTBF and had been tested and approved by a third party.

Asedr said, the SIL2 or SIL3 means a complete safety system which means that every single part in the loop, starting from transmitter through barriers, logic solver, wiring method and ending with actuator must me in compliance with safety standards.