One option could be to reference a stylesheet in module config, with the name set to "navigation".

  <clientResources>
    <add name="navigation" path="Styles/UiStyle.css" resourceType="Style"/>
  </clientResources>

This will render the stylesheet in both edit and admin mode.
You could then change the appearance of the rainbow colored line like so:

.epi-navigation-expandcollapseContainer,
.epi-navigation-delimiter  {
    background: red !important;
}

This will make the line bright red, which should be fairly visible for all users.

If you're using some kind of configuration transformation (so that the UAT environment config-files are automatically created for deploy) there are plenty of things you can do.

With specific flags you can output specific .css files (Skuseth's example for EPiServer interface) but also in your templates.

Thanks for the suggestions. Sounds easy enough to implement that with our post deploy script. Will give it a bash!