source1import VS srctools

If your map contains custom models are not in the base game (this means you created, imported or downloaded from any else), you need sure to use source1import or recompile the model from scratch to new Source 2 models and textures with the new tools and add to custom addons folder.

The way it works is that the vertexes in the file may not necessarily be any vertexes on the brush themselves (though hammer does seem to have them match). As you kinda guessed, the three points define a plane for each face. Edges and vertexes are then produced by intersecting all the planes with each other - 3 would define a point. This is why you can't have concave brushes and why there's the vertex drifting when saving weird geo. It's quite awkward to obtain vertexes, but it does allow very easy collision checking - simply check if your point is behind all the planes, and if so it's inside the brush. There's some more documentation on the VDC. If it helps, I have some mostly functional Python code here decoding out the vertexes of a brush.