But, as you might have noticed. It is possible to get through using uranium and something creating a LOT of pressure so the uranium keeps its temperature. This, however can only be done with clone.
So my suggestion is to make bunkers safe against bombs only consisting of materials that can be used in the bunker, i.e. no walls. No diamond. no clone. etc...
Well , we can all make a "Bunker" with 100 layers that take 3/4 of the screen that ain't hard but lets try and make a bunker that uses as least layers at it can while not beeing destroyed by the 2 Stage-Nuke. As far as i know is the most real "Nuke" and the most destructive. Pouring mix of lava and heated Uranium on any Bunker will destroy it but lets use the 2 Stage-Nuke as a Scale , also no "implosions" ( as i put the nuke inside) a bunker keeps the inside safe not the other way around. Also when you are done with your bunker you should put some Goo forms inside and consider them the Test Subjects if they survive after the blast and aftermath ( that if the bunker starts to melt away) you got yourself a nice bunker , but keep in mind we want a bunker not 100 layers of different metals and insulators on top of eachother.