I cannot comment on your contention since I am not aware of the complete thought process that leads you to the conclusion, but I would prefer a warren to mere bunkers.
I would take the US as a 'superior force' any day (nad for a very long time indeed) and I reckon it is worth learning from the Taliban or AQ experience in Tora Bora where the caves saved many of those blokes, even though it would have been preferable that the caves not save the Taliban and AQ.
Tunneling and warrening is not something that one should be ashamed about. In fact, those who can do so, are actually fantastic.
If properly camouflaged, one would never know that troops are there and those who attack can be badly surprised, even in the contemporary scenario and technique of warfighting!
The concept of missiles in silos is passe. Being static it is a dead duck, in a manner of speaking. Mobile launchers are dernier cri