I covered my entire switching layout with Homasote. Then raised the mainline and siding with more homasote and/or cork. All the industry tracks are on top of the base layer of homasote creating 3 different levels of track, just like the real world.
Most yard tracks are ballasted with small crushed rocks, significantly smaller than mainline ballast, and covered up to the rail for the most part. Depending how you plan to ballast the yard tracks, it will just require more ballast whether or not you use cork. If you have QB or Homasote as a base, I would attach the yard tracks directly to that. Just my opinion.
You can see all these yard tracks are "burried" in the dirt. When we walk around in the yards, the ground is level with the top of the ties. We just have to step over the rails.