I have recently done a screen replacement of my own Google Pixel 6 myself, and I also struggled with this issue, but managed to get it working in the end.
The reason the tool isn't seeing your phone is probably because you need to download the Google USB driver. I did not find a way to use Linux for installing the driver, so probably best if you use Windows for this.
I found the answers of my issue in an iFixit article, so I recommend taking a look at the solution in the article.
Two things I did not understand from the article at first was that I needed to use Windows and where I could download the driver, but when you managed to install the driver successfully and boot into fast boot, your phone should display in the Pixel calibration tool.
After that you should run the tool twice like de0u said and your fingerprint scanner should work again.
Good luck and I hope this works for you. Otherwise I'd recommend contacting the seller where you bought your screen from as this isn't a GrapheneOS issue only, because Pixels with the stock Google OS also have these issues after a screen replacement.