I just did the math on their entry level model because I didn't believe you, but you're pretty close with that estimate. NewEgg prices:
Threadripper 3960X - $1400
16GB 3200 RAM - $70
256GB NVMe - $70
RX 550 - $70
= $1600System76 price = $3700
That said, if you're looking at their higher-end models, I think you still have a fixed ~$2k markup, and so you're looking at something like $10k vs $12k, which isn't a big deal for that sort of customer (does save time, after all).
Side note: I own their AdderWS laptop and am a happy customer.