These are a lot more expensive and difficult to deploy. They weigh several tons. You can't just strap one to a $200 quadcopter and fly it over.

You don't dig a hole deep enough that Bunker Busters can't penetrate. You drive up to the root of a mountain where it meets flats and drill sideways. Getting your men out in case the entrance was bombed can be tricky though.

to use a GBU-28 or similar you need to establish air superiority first

The current crop of "cruise missiles" are cheap and low penetration. Burying things is not 100% safe, but it certainly increases the attack difficulty.