We compute Fourier-resolved X-ray spectra of the Seyfert 1 Markarian 766 to study the shape of the variable components contributing to the 0.3-10 keV energy spectrum and their time-scale dependence. The fractional variability spectra peak at 1-3 keV, as in other Seyfert 1 galaxies, consistent with either a constant contribution from a soft excess component below 1 keV and Compton reflection component above 2 keV, or variable warm absorption enhancing the variability in the 1-3 keV range. The rms spectra, which shows the shape of the variable components only, is well described by a single power law with an absorption feature around 0.7 keV, which gives it an apparent soft excess. This spectral shape can be produced by a power law varying in normalisation, affected by an approximately constant (within each orbit) warm absorber, with parameters similar to those found by Turner et al. for the warm-absorber layer covering all spectral components in their scattering scenario. The total soft excess in the average spectrum can therefore be produced by a combination of constant warm absorption on the power law plus an additional less variable component. On shorter time-scales, the rms spectrum hardens and this evolution is well described by a change in power law slope, while the absorption parameters remain the same. The frequency dependence of the rms spectra can be interpreted as variability arising from propagating fluctuations through an extended emitting region, whose emitted spectrum is a power law that hardens towards the centre. This scenario reduces the short time-scale variability of lower energy bands making the variable spectrum harder on shorter time-scales and at the same time explains the hard lags found in these data by Markowitz et al.