I would seriously do what addy has drawn; I didn't have access to this forum upon my initial dig and regretted the fact I could see my liner for almost 8 years. I did end up finding natural covers with plants, but it takes time for them to grow in and well, spring always was very unforgiving of my mistake. You know, when you build something and you KNOW where the mistakes are even though no one else does...well, I surely fixed all that with my expansion.
You state you have lots of extra liner--that's the smartest thing you've done yet. Use it; dig that shallow shelf, it doesn't have to me more than 4" wide but don't make it more than 3" down or so. This gives you tons of options, plants included. If you don't want the slate type perimeter, you don't have to do that but you can put any size rock now (even allowing it to cantilever though I wouldn't). If you know you're going to use larger rocks, say 8-12" size, make this VERY SHALLOW shelf that wide. It also allows you to mix the size rocks you use to make it less uniform. You can add gravel as you suggested, and plant marginals as their feet will be in the water but stems close enough to the surface to thrive.
This one piece of advice, in my opinion, really separates the amateurs from the pros; hide the liner if at all possible if you want it to look most natural. Best thing I did upon expansion.