You have to remember that we provide support to people around the world at many skill levels. We also provide support with generic information and provide basic information so that everyone, not just you, can find the answer they need. Sometimes, the help answer may appear basic, but that's because we also don't know your skill level either. Remember, as you've found out already that Trainz can be quite complex even though it's supposed to be a game.
The issue is the textures, but I wasn't sure if you were aware of the height settings, and this issue has nothing to do with the new Surveyor 2.0.
The new PBR textures, such as the built-in ballast, grass, and rock textures, have height information built into the textures to give them a 3d look to them. The issue here with the PBR textures is they raise the height of the terrain and then the terrain goes over the track as you have encountered. In other instances, there are spaces below the terrain making the track appear to be floating when it's not. One of the solutions is to use a wider texture brush when putting down the textures under the track. This will smooth out the terrain and remove the raised portions, well it's not really removing them and only spreading them out a bit more.
The alternative is to turn down the Shader performance, found in the Trainz settings tab on the Launcher under performance, to standard. This requires a restart so don't do it while you have a route open. When you open your route then, the PBR effect is no longer there, and the same textures work as if they did in TANE.
It's not that PBR textures can't or shouldn't be used with the Shader set on high, it's they take a lot more work and practice, and for those of us who have imported old routes we worked on a decade ago, they create a sad mess that needs repairing. If I were to start a new route from scratch, I would definitely use PBR textures because they can be quite nice.