Except that breakdown is wrong. ( Assuming there is no mistake in Mac Pro Spec )
The CPU isn't a Xeon W, while there is a Xeon W with 8 Core, 3.5Ghz and 4Ghz Turbo, the W3223 $750 as used in calculation, it only has 16.5MB of L3 Cache. The Mac Pro listed the 8 Core with 24.5MB cache, that is only available on the Xeon Gold 6234 model, cost $2200. Xeon Gold also gets additional AVX512 Unit, so it is quite different in FP power compared to W3233.
The problem is 6234 base Clock is only 3.3Ghz, and Turbo at 4.0. Doesn't fit Apple's Description. The only other candidate is 6244, which has a base of 3.6Ghz and 4.4 Turbo costing $2900. I am going to assume Apple has a custom Chip, so let say this thing cost $2400?
That is automatically an additional $1200 on top the original $3160 calculation.
There is the Black (?) Magic Keyboard and Mouse Included, $250.
So far all the Pro's has at least 3x3 802.11ac 1700 / 1900 Mbps WiFi Speed, assuming this is what the Mac Pro has included ( doesn't list the speed inside the spec ) and Bluetooth 5.0, that is additional $100.
That prices doesn't include the 4x Thunderbolt 3 Port, which is ~$150 ( depending on chipsets )
That is in total now $4860.
The Radeon is actually a Pro Series with X Ending. Using a R580 as base price hardly seems fair, especially when the cost in Pro series are the drivers. ( You can see how Quadro on Nvidia are much more expensive ) Along with Massive Heat Sink, T2 Chip, which in itself is like a Raid Controller for SSD along with encryption. Windows 10 Professional if you bought it from other Vendor. I mean the Windows 10 alone is $200. All of the above is easily another $400.
All of a sudden you are looking at $5260, not including the built quality.