It sounds like the prebuilts put a lot into gaudy, visible stuff that looks good in the product photos like lots of RGB LEDs and cheap out on less visible stuff like noise levels and adequate rear I/O.
If you aren't getting "adequate rear I/O" then go looking for a prebuilt Threadripper Pro system with $700 motherboard. There will be plenty of ports. They have to do something with 128 PCIe lanes.