I rather doubt anything above ground could be trusted to ensure the Pope's survival. EMP is a bitch especially when applied to complex machinery such as aircraft.
While the shelter and underground rail options are plausible, in my opinion the best, safest option is simply not to be there in the first place. Perhaps a double was used in the last few weeks/months and the Pope "telecommuted" from a much safer location elsewhere on the globe?
The Pope, and the church in general are certainly not nuclear targets in and of themselves, but the Vatican is in a rather vulnerable position being located in the capital of one of the major belligerents. While not exactly a huge issue in WWII, the exponential increase in destructive potential of weapons 50 years later is something else entirely.
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If it moves, shoot it, if not push it, if it still doesn't move, use explosives.
Nothing happens in isolation - it's called "the butterfly effect"
Mors ante pudorem
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