Gold coating is a routine process before carrying out SEM on a nonconducting sample. Since this sputtered gold film could also be a source of features which are not part of sample, i would like to know what kind of artifacts we may get.
Mainly depends on the thickness of the sputtered film. Even with sputtering, gold form islands at thicknesses roughly below 20 nm. So, you should be aware of the non-coated areas, for they could charge easily.
If you go thicker on the other hand, and sputtering makes it even worse, substrate surface becomes rough. This means what you observe under OM/SEM/AFM is likely quite different from the actual topography. Annealing is an nice option of course.
To get the best result, coat with ~20 nm Au, and anneal at around 100ºC for 2 min. By this way, both the surface will get "flatter" and possible open areas will reduce/close up.
Modern peak deconvolution algorithms can separate elements with overlapping peak which allows displaying the element distribution of these elements. However, the quantification results will show larger errors. Gold is a heavy element, thus, the low energy X-ray lines will be absorbed more when compared to the high energy X-ray lines. This results in lower values for low energy X-ray lines and higher values for intermediate and high energy X-ray lines.
Due to this fact and overlapping peaks of gold with elements to be analysed, it is recommended using carbon coating instead of gold. An alternative might be aluminium , if this element is not represented in the studied sample.