My Firefox does as well.

Anyway, it seems to just work by drawing over it:
<details><summary>Sample Python code</summary>

```python
import math
import gi
gi.require_version('Gtk', '3.0')  # noqa
from gi.repository import Gtk


# Interesting piece
class MyScrollbar(Gtk.Scrollbar):
    def do_draw(self, cr):
        Gtk.Scrollbar.do_draw(self, cr)

        alloc = self.get_allocation()
        cr.set_line_width(1)
        cr.set_source_rgba(1, 0, 1, 0.5)
        for mark in (0.05, 0.2, 0.5, 0.55, 0.8, 0.9):
            cr.move_to(math.floor(alloc.width * mark) + 0.5, 0)
            cr.line_to(math.floor(alloc.width * mark) + 0.5, alloc.height)
            cr.stroke()


# Boilerplate follows
class Window(Gtk.ApplicationWindow):
    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)

        self.scroll = MyScrollbar(visible=True)
        self.add(self.scroll)


class App(Gtk.Application):
    def __init__(self, *args, application_id='test.ScrollIndicTest', **kwargs):
        super().__init__(*args, application_id=application_id, **kwargs)

    def do_activate(self):
        window = self.get_active_window()
        if not window:
            window = Window(application=self, default_width=600)
        window.present()


if __name__ == '__main__':
    App().run()
```
</details>

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