Writing a Custom Collider

I am currently in the process of creating a game that uses procedural heightmap terrain generation. Originally, the terrain was made through a MeshObject built from scratch from verts and tris, but building the collider was much too slow. Fortunately, Unity soon released the Terrain system, which can build terrain with a heightmap in much less time. Unfortunately, Terrain refuses to play nicely with procedural generation, so everything from setting textures to aligning seams is apparently impossible at runtime. I've set out to write my own terrain system. I know how to build the mesh and manage the terrain and everything but there is still one problem.

Long story short, I have no idea how to write a custom collider without using the MeshCollider system (which is seemingly not optimized for 2D heightmaps). Is this even possible? Alternative heightmap-based procedural terrain methods are also happily accepted.