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Just as in InFamous, or Just Cause 2, navigation is as much vertical as it is. The military base is just included so that your character can gain experience. In Assassin's Creed II, of the 200 missions, about half are side quests. Since there's no real time limit for completing the game, it is not required. The car is mainly a convenience issue - it speeds up overland travel.
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It won't assume that you have it until you've reached Vault City (however, you can still complete all of the things mentioned, although it is a lot harder), but after you've got the car (after that section is covered), the walkthrough WILL ASSUME that you have it. This walkthrough will include (very early on) information to get the Power Armor.
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