This is difficult to fix because the drawers are planned to be kept independent of the LCL as much as possible, and wanting to replace system colors by the rgb values would mean to call the function ColorToRGB from unit graphics. However, the drawers are constructed quite flexibly: there is a function pointer DoChartColorToFPColor which converts TColor to the TFPColor values used internally by the drawer. Normally this points to the function ChartColorToFPColor which simply extracts the r,g,b bytes from the TColor and assigns them to the Red, Green, Blue words in TFPColor. Alternatively you can make it point to ChartColorSysToFPColor which does the conversion of the system colors first - of course, at your responsibility because now the drawer calls an LCL function.
The drawer is accessible as Chart.Drawer, and thus, when you add the following lines the blackness in the aggpas chart will be gone (you still need to update to the current TAChart units because several issues had to be fixed for this to work):
uses
TADrawerCanvas;
procedure TForm1.FormCreate(Sender: TObject);
begin
Chart1.Drawer.DoChartColorToFPColor := @ChartColorSysToFPColor;
end;