Extracting kinematics from stellar spectra. Why are template stellar spectra necessary?
(Optically thin) Emission lines in nebulae are generally unresolved and have simple shapes that might be approximated by Gaussians. Stellar spectra are complicated - there are blends, there is rotational broadening, the lines are not Gaussian, there are molecular bands, there may be two stars!

By cross-correlating (or fitting) a template you are effectively modelling your spectrum with what you already think is the best representation of the spectrum.

If emission lines are not unresolved and show velocity structure, as you say, then fitting a simple Gaussian will give an incorrect result. A more complex model would be required, but as far as I know there are no template spectra that can help you out here. The situation might be thought analogous to a stellar spectrum with rotational broadening, but there the template can simply be convolved with the appropriate rotational broadening kernel.