Not doubting the price you were seeing in NewEgg, but find it hard to believe you couldn't build your own PC with the same CPU and equivalent RAM, GPU, cheaper by sourcing the parts from retail stores yourself.
Was it a case where Apple was getting an incredibly good deal on those?
Yes, they basically bought up the entire market on those Xeons, and that 2008 line was THE Mac Pro to buy into. I'm still using it today, zero issues! Except of course the whole Apple no longer supporting it with their Sierra OS. There were articles on it comparing sourcing yourself, and you really couldn't just throw together a workstation grade PC like this for that price.
$3000 got you 2 x 2.8ghz Quad core Xeons, up to 64GB of FB-DIMM ECC, 4 x drive bays + 2 x CD bays.
There isn't much this thing still can't handle, it's just being phased out, and eventually it won't turn on one day.
Was it a case where Apple was getting an incredibly good deal on those?