There’s a parameter called “uplift” in your erosion device. What happened is, you eroded terrain with “geological time enhancement” enabled, that exaggerates the erosion effect artificially, lowering your terrain. There’s a slider named “uplift” right below that checkbox, it raises your terrain to fit the channels properly into your terrain. This is available in the latest stable build at least. That example must be from before that feature was implemented. Project may need a complete “device version” update for new settings to appear. If you’re okay with it, PM me the project. I’ll fix it for you tomorrow.
As for the lake, I personally build my lake geometry separately. Layouts are good for blocking shapes, but a bit too crude for plugging in directly. Add a noise, and then some sparse erosion to it, and it’s ready to be combined after. Or before, if you have water in your scene. Lake needs to be plugged in “after flow restructure”, and “before create water”.
I’ll block out an example with correct usage tomorrow, it’s a bit late over here. You can already plug in water to most of your erosion devices, so that it all flows in a unifying fashion. It’s just the “order” that needs some thinking.