I'll try to answer your questions, but more information and/or specific scenes or image examples may be needed for better problem solving.
1: The sequence of shaders can be very important to the final results. Shaders further down in the network cover and act on the ones that precede them. You would use shaders before the "compute terrain" in any situation where you are only intending to add displacement, not color, to the scene. Displacement should always, when possible, be done before the Compute Terrain as this makes all shaders after it work more accurately to the shape of the terrain.
2: This is probably due to the Redirect shader being used in conjunction with a Displacement shader of some kind, which changes the shape of the terrain. If your population is not set to key its "sit on terrain" setting off of the last shader in the network, it will not place plants correctly. Additionally if significant displacement is performed *after* the Compute Terrain in the Terrain group, you will want to put in another Compute Terrain/Compute Normal.
3: You can use a blend shader composed of an inverse of your larger Fake Stones layer to keep your other Fake Stones from overlaying them.
4: The water level curves with the planet unless you tell it not to. It will be less accurate further from the coordinate origin I believe.
- Oshyan
