Yes, the time series load provider uses linear superposition. If that assumption is not valid, then you may need to use the time step load provider.
Technically the stress-life method (SN) is only valid for elastic stresses, although its application is sometimes stretched to be used when the elastically calculated stress is slightly above yield. SN is not valid if the stress is significantly above yield.
With time series loading, the fatigue stress is the FE stress multiplied by the time series scalars. For SN to be strictly valid, that stress (FE*time series) must be less than yield. If elastically calculated stress is significantly above the yield stress, you should use the strain-life method (EN).
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