Most of the cracks in quartzite at faucet holes are caused by excessive heat when drilling the hole; this is fabricator error. I doubt your hole was drilled on the CNC machine wet; it was probably drilled on site dry. Sometimes the operator doesn't anticipate when they're about to go through and the grinder slams into the deck when it finally does. It wasn't caused by over-tightening the faucet.

Short of replacing the sink with one with a faucet deck, there isn't really an inconspicuous repair. Decontaminate, tap in a little super glue, scrape to flush, and call it good. Fortunately, it's going to look like a natural fissure.

See if you can slide a steak knife between your sink flange and the bottom of the stone in several places please. You should not be able to. It doesn't appear that there is any silicone between your sink and stone. If there isn't it cannot be effectively applied topically. The sink must be dropped, the flange siliconed, and the sink reinstalled. As you look underneath, see if there is silicone squeeze-out at the sink perimeter; there should be plenty. If there is no silicone at the sink, that's a big hint as to the quality of your fabricator/installer.