I agree with you on "yield" but I would caution you on the option of "deeper penetration". Simple physics tells us that we can´t "plan for" or "arrange" for deeper penetration.
Assuming the same material and bomb structure, the only way you can penetrate deeper is a higher velocity of the bomb. That of course will place a higher stress on the bomb equipment. Meaning that you run the risk that a part of the equipment might malfunction or - in a worst case - the bomb will simply break up.
Meaning that for a target buried deeper, you would have to use a higher yield nuclear bomb. Which will of course mean a much higher level of radioactive contamination above ground. :(
From what I´ve read on the Internet, all current American nuclear bunker busters rely on gravity to accelerate. Meaning that they don´t have a rocket engine, you simply release them from a high flying airplane and rely on gravity to build up velocity. There´s no way that such a bomb could bury deep enough and not release radioactive contamination even at low yields.
Second I'm guessing that bunker busters and the like have several stages. The first probably blows a hole into the ground so that the main part of the bomb can penetrate further. It is also possible it just could sit there and drill down. Who is going to stop it? Policies not Politics ---- Daily Landscape
I never intended to leave the impression you could bury the weapon such that no radiation would escape into the atmosphere. As you say, that can't happen.