An additional factor you’re going to want to take into account is how the device is going to be delivered to the F-Bunker. The only way to feasibly do it in 1945 was to drop it out of a B-29. Depending on a variety of factors (if the B-29 is getting shot at or not, weather, visibility) this can either be quite accurate or miss by several miles. At Hiroshima, the bomb missed the aiming point by 800 feet; at Nagasaki, the Fat Man bomb missed its planned aiming point by nearly 2 miles. As already noted, both bombs were airbursts, in order to maximize their destruction of the lightly constructed buildings typical of the area. To destroy hardened targets such as missile silos and C3I bunkers like the F-bunker, you’d typically use a groundburst, Given that the Fat Man bomb was not a hardened, armor-piercing design (OTOH, the Little Boy design was, IIRC, supposed to be very robust, if extremely inefficient), you’d probably set the bomb to detonate as close to the ground as practical without actually striking the ground.
We have data for the effects of prompt radiation on animals within bunkers from tests like Crossroads and others at the Nevada test site. During the Able test at Bikini atoll, a bomb very similar to Fat Man was detonated over a collection of ships. Animals were caged within the ships to serve as test subjects for bomb effects. Within one of the ships, the decommissioned battleship U.S.S. Nevada, animals were caged within the battleship’s turrets. The turret was protected by 18 inches of armor plate. The Able bomb detonated roughly 700 yards away, and 520 feet above the water. Despite the large distance and 18 inches of steel shielding, a goat within the turret still received enough radiation to die of radiation sickness 4 days later. The distance was far enough away, that the crew of the bomber which dropped the Able bomb had a board of inquiry convened against them for negligence.
From The Nuclear Weapon Archive comes a set of equations for roughly scaling the effects of nuclear weapons. For the Able bomb of 23 kilotons (or, roughly the same yield as Fat Man) plugged into those equations yields a distance for receiving 500 rem (5 Sv)of prompt bomb radiation of ~1500 meters. This is if you were standing in the open air. The wiki for radiation shielding gives some figures for “halving distances”: the thickness of material needed to reduce radiation by 1/2. As different types of radiation penetrate different materials more readily than others, this is necessarily a gross estimate. Still, from the linked chart under radiation shielding, the figure for steel is 1 inch. So, if the goat on the Nevada was sitting behind 18 inches of steel (which seems awfully high, but that’s what the wiki for Nevada had listed for turret protection), then the radiation reaching the goat was attenuated by 1/(2^18), or nearly 250,000 times. My guess is that there wasn’t 18 inches protecting the goat and that armor steel’s halving distance for Able’s radiation is greater than one inch. If we take the chart at face value, then plugging in 4 meters of concrete and 8 meters of dirt gives a total of roughly 150 halving distances. Or attenuation of 1/(2^150). Taking the linked radiation protection chart at face value, I don’t think they’re going to take too much damage from prompt radiation in the F-Bunker, unless you dropped the bomb directly on top of the bunker.
From the nuclear weapon archive’s discussion of the Buster-Jangle series of U.S. surface nuclear weapons tests, it was extrapolated from the “Uncle” test of a 1.2 kT sub-surface device that a 23 kT gun-type penetrating device would leave a crater 700 feet in diameter and 140 feet deep. Naturally, the size of the crater would depend greatly on the nature of the excavated soil, as well as how deep the weapon buried itself before detonating.
So, my guess as to what would happen if the Allies nuked Berlin is that the Allies would use an airburst and the F-Bunker inhabitants would survive, absent a firestorm being created by the device. (Not that there was a great deal left to burn in the Berlin of May 1945) If the Allies tried to kill the F-Bunker, then they’d use a near-groundburst and hideously contaminate most of downtown Berlin with radiation. Not to mention splattering the Soviets with a lot of downwind fallout. Your guess is as good as mine as to how close they’d have to drop the device to kill the F-Bunker with a ground burst. I think a drop with Hiroshima accuracy would do it.