But could the scrollbar at least be more independent from the native theming?

Again, GTK theming can achieve that, in conjunction with the widget names we set explicitly just for that reason. You could do e.g. something like that (alter as pleases you):

style "geany-scintilla-scrollbars"
{
  # select any non-pixmap engine if your theme is using pixmap like e.g. Adwaita does
  engine "clearlooks" {
    style = GLOSSY
  }
  # and choose the colors you like (possibly also alter "fg", depending on the engine) 
  bg[NORMAL] = "#333"
  bg[PRELIGHT] = "#444"
  bg[ACTIVE] = "#666"
}
widget "*Geany*Scintilla*Scrollbar" style "geany-scintilla-scrollbars"


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