Seems to me that instead of digging a tunnel, you could get the same protection from ISR by building those road coverings out of corrugated metal, plywood, or even just laying vines over them. The benefit of the vines is they are cheap and could regrow after a drone hit.

Also, in addition to underground and outer space, we should consider underwater. Underwater bases would be safe against most missiles and drones. Cargo submarines could bring gear to our bases safe from drones and anti ship missiles. And we may want to revisit the idea of a submarine aircraft carrier but with drones instead of manned aircraft.