I'm interested to know if these things will actually work against newly built facilities, or if the people engineering the bunkers have actually taken into account the kinds of weapons that might be deployed against them, which you assume they would particularly after seeing what happened to other existing designs.
The old WW2 submarine pens were pretty much bomb proof - as I remember it the facilities where construction was finished, and all the parts of the protection were in place were never successfully penetrated even by the largest of the dedicated Tallboy bomb designs. Only those pens that were incomplete and missing the upper protection structures were seriously damaged. The design of the pens took into account the weapons that would be deployed, and countered them. The same is likely to be true today.
Given that the concept (and in some cases the detail) of the various pentrator bomb designs is well known (generally variations on the original gun tube based design), it isn't going to be a huge challenge to produce a bunker design to counter them. And after all, the design challenge isn't going to be too different to that involved in vehicle armour designed to stop penetrating rounds.
I suspect that the right layout of alternating concrete, steel, composites, soil, voids, shaped deflection layers and an anti-spall liner would be adequate to stop one of these things. Even the 'smart' detonator designs could potentially be countered with the right layout. The kinetic energy of the impact will make some damage inevitable, with a big mess on the surface and for some distance underground, but the bunker complex itself could survive with no internal damage.
Even attempting to attack the 'soft' entrance of a facility might not be viable, as it can either be hardened directly, or more likely you could contruct or site the entrance in such a way that a direct attack is impossible as you could ensure that terrain or structures would block the trajectory of any incoming weapons.
Penetrating even thick layers of soil, rock, and mass reinforced concrete is relatively trivial, as is pentrating armour steel. But it's entirely possible to engineer something that would slow, deflect or disrupt a pentrating projectile to such an extent that it becomes ineffective. And when you've got many metres of space to play with to build your bunker roof, it's easy to add all kinds of tricks into the design.
I'm sure these weapons will look the part, will make for some impressive demonstration videos and will be quite capable of erasing an older bunker, but it's quite possible that the newer facilities won't be such soft targets.