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That's normal and annoying Trainz behavior that has occurred forever. If you offset an object 20 meters from the ground, this is in reality 20 meters from zero. You then move the same asset to another place on the map that has a 40 meter hill. The asset is still at 20 meters from zero so when it hits the 40 meter hill it ends up being buried.
Trees are supposed to do that. Most scenery like rocks, boulders, and houses, for example, can/will sink into the ground. That's why there is a height function in Surveyor. Probably a tag in config, or from the class it inherits from.