Layers allow session makers to do much more than was possible in earlier editions of Trainz.
For example, prior to TS2010 if a session needed, say, route markers and triggers to work, the only way to achieve this was to add these to the route. If the intent was to share the session with others, the modified route had to be uploaded to the Download Station.
Now markers and triggers can be added to the session, the route remains as it was, and only the session needs to be uploaded. See, for example, my post here: