javierac - numerically we can perform an FFT on any waveform we choose, periodic or not. How we should interpret the result in case of nonperiodic signal is a question worth asking, as you point out.
One way to interpret a FFT=DFT is as the discrete fourier series representation of the waveform which is a "periodic extension" of the original waveform. So if we sample 100 points, then we assume we have 100 samples of a waveform which continues to repeat itself every 100 samples and determine the discrete fourier series of that periodically-extended waveform. That can introduce errors whether the original waveform was periodic or not... For example if we sample a periodic waveform V=cos(2pi*f*t) for an interval from 0 1.5/f (one and a half periods), and then recreate that periodically, we have a discontinuity jump in the waveform which creates high frequency content that was not present in the original waveform. Windowing techniques are designed to reduce this kind of error.
There is yet another way to interpret the FFT=DFT. A transient waveform will have a continuous fourier transform (what you would see if you input into perfect spectrum analyser). That reflects the fact that a transient nonperiodic waveform CAN be decomposed into an infinite number of sinusoids (not sinusoids at discrete frequencies). For example exp(-alpha*t)*u(t) transforms to 1/(alpha+jw) which does not represent a single frequency or several discrete frequencies, but a contribution from infinite number of sinusoids. FFT/DFT is NOT capable of representing this type of continuous infinite number of frequencies, since it represents discrete frequencies. But the FFT=DFT does represents frequency "samples" of the continuous fourier transform sampled at frequency intervals of somewhere around 1/(2NT) where N is number of samples and T is time duration of the waveform.
In the case of transformer inrush, as has been discussed, there is at least one very useful application, which is examining how harmonic restraint can be used to differentiate a fault from an inrush.