The 'Afterburner card' isn't present in the base configuration of Mac Pro we know the price for.
Dell can add an NVMe SSD, wifi, bluetooth, 2x10 gigabit ethernet, and a keyboard and mouse. Those increase the price by $400. Dell will do two thunderbolt ports for $70, so 8 would be $280.
So unfortunately the things you've listed only explain $680 of the price difference.
Yeah, like I said, a lot of the difference seems to be that yours is a Precision 5820 and Gizmodo's is a Precision 7920. Understanding the reason for the price difference there is probably pretty relevant to this.
Dell can add an NVMe SSD, wifi, bluetooth, 2x10 gigabit ethernet, and a keyboard and mouse. Those increase the price by $400. Dell will do two thunderbolt ports for $70, so 8 would be $280.
So unfortunately the things you've listed only explain $680 of the price difference.