Yes, they’re deprecating decent products in favor of inferior new ones. And seemingly pushing new code repos, too.
With the caution that barebones USB concentrators (ie, FT2232 rather than an MCU as in the pico GW design) have issues, mostly what you need is either an old version of the LoRa HAL that still has USB, or a current version that someone’s stuck the USB support back into.
For example https://github.com/RAKWireless/lora_gateway
The repo you’re not managing to find is more of a meta-repo that handles the installation - the actual work is done by the lora_gateway HAL and the packet fowarder repo, for which you can probably use either RAK’s or Semtech’s, albeit possibly with some slight compatibility issues.
Since your pi has SPI you might consider switching to that mode, though you’d need to tap out the SPI signals at the base of the mPCIE connector, and ground pin 17 to put the RAK833 in SPI mode.