Not necessarily. A "stock" 747, without any of the extensive enhancement necessary to serve as AF1, costs over $400 million (and that's not counting the cost of the engines - long story why). The AF1 cost also undoubtedly includes development costs for the technologies involved, all of which is spread across two aircraft instead of thousands, as in the case of civilian versions.
I think Trump is actually using this example more as a shot across the bow to let defense contractors like Boeing know that when we begin rebuilding our military capability, they shouldn't expect it to be a free for all. There will be extensive oversight to ensure that the value for our tax dollars is maximized. I'm pretty sure that was what he was getting at.
A ‘stock’ 747 might be *listed* at that price but no one pays list price...except maybe the federal government because it’s not their money, they’re terrible at negotiating, and for certain other products negotiation is outlawed due to company lobbying.
Common discounts on Boeing and Airbus planes for the commercial sector are in the 25-60 percent range depending on model and customer order volume.
Defense contract costs, as well as many other things that the federal government buys, are mostly never justifiable. The US government is routinely ripped off and it’s usually intended to be that way.