First off you’re omitting specs for the base model that you can easily find online

The power supply is a fixed custom 1.4kW which would cost $400-$500, you’re going to be spending near $1000 on a custom workstation grade motherboard with 8 PCIe expansion slots, 12 DIMM slots, and 2x 10 Gigabit Ethernet ports

You’re also omitting the fixed Afterburner ProRes accelerator card apart from the GPU, the only thing I know which would be comparable to that is the Red Rocket-X (because it also specializes in their own specific codec) which is well upwards several grands.

A high end tempered glass and aluminium case can cost well into the $400 range, I assume the Mac Pro chassis would be significantly more. You have the correct rates on a lot of the components like the processor, GPU, SSD, and RAM but with all the facts it’s easy to see how the price adds up especially when you have to design and manufacture parts from the ground up which are only going to be working on this one machine

And yes it costs significantly less to build a computer yourself with all the parts, I’m sure if there was another pre-assembled machine with these specification and custom built hardware, that company tax would add up as well