Setting both "System"
and "Global"
sub-option values at once seems to work:
SetOptions[EvaluationNotebook[],
"AutoStyleOptions" -> {"SymbolContextStyles" ->
{"System" -> RGBColor[211./255, 54./255, 130./255],
"Global`" -> RGBColor[181./255, 137./255, 0./255]}}]