It should be possible to set colorScheme and individual properties at the same time. For example:
 

theme: GraphsTheme {
  colorScheme: Qt.Dark
  backgroundColor: "#ff0000"
}

 
Should result dark theme with red background. Currently if QML engine decides to evaluate colorScheme after backgroundColor, it overrides the backgroundColor. Old 2D graphs implementation used m_customFlags for this (https://codereview.qt-project.org/c/qt/qtgraphs/+/557624/9/src/graphs2d/themes/qgraphtheme.cpp#b223)
 
Same thing with theme, this:
 

theme: GraphsTheme {
  theme: GraphsTheme.Theme.MixSeries
  seriesColors: ["#444444", "#555555", "#666666", "#777777"]
} 

 
Should use seriesColors, although it doesn't make much sense currently unless theme starts to define also seriesGradients, borderColors or something.