I wouldn't say they are priced similar. The ATS is a true custom made road race header and costs 3k. Thats not 2k(DSE). Custom built pipes are in the 1200 to 1500 range in mild steel, add high quality stainless/o2 bungs/v band hardware you quickly surpass 2k. My Dan Lemons big block chevy pipes were over a grand in mild steel.
To get this stuff to fit your custom chassis is the hard part, Its pretty expensive, I see your point to a certain degree. But the additional costs of the fuel injection and associated electronics, serpentine accessory systems, and custom made pipes can all add up the same on a gen 1 as well. I have a full FAST system on my sb and it cost a bloody fortune to set up. If you do a vintage air frontrunner sysem on a sb its gonna be bucks.
Tell you what I just picked up a complete serp system from gm performance parts for 450 bucks for my ls7, I feel like I got the bargain of the century, it certainly doesn't look the best but it has a stock looking appeal.
Rich