Thanks for the feedback Sembazuru. The coloring thing is purely non-intentional because I am 'hacking' the paint routine, so it automatically presets the coloring.
I tried to include the line numbering system from jEdit (Arduino IDE pane is based on jEdit controls, and jEdit right now is light years away with enhanced scroll, collapsive blocks, numbers, etc) but due the dependencies it is a major rebuild to update that panel. So what you tested it is a very quick and dirty attempt (1 hr or so).
So I still I am unsure how to handle the line number space, dynamic or static. I think the style of the panel can be added to the theme folder maybe (like background color, number color). Also will check the horizontal scroll, didn't noticed that, and it seems be very important due the way this hack works. It might need to do another trick like moving the textpane a little to the right, not inserting the numbers inside the text and sync both controls.