I don't know if the contract says that the KC-46 cannot scrape a stealth airframe or if the issue is that sometimes the boom operators do not detect that they have scraped an airframe (which has happened). Boeing is working on improving the contrast of the Remote Visual System so operators can better detect when a scrape has occurred.
I admit that we will try to make sense of this, but really based on what we know, military a/c spend more time in maintenance after normal ops, I would be shocked that they do not inspect refueling contact points on a periodic basis, heck even when I watch video's of the process you can sometime's see the contact.
I guess the next thing would be quantifying how much fuel is lost when the boom disconnects and we see that spray of fuel.
The scrapping issue has been around since the days of the KB-29P and KC-97. Even the KC-135 and KC-10 has been known to scrap receiver aircraft, including strealth aircraft like the F-117, B-2, F-22, and F-35.
The difference here is both the KC-135 and KC-10 refueling is viewed through a window, and not cameras and TV screens of the KC-46 (BTW, the A-330MRTT/KC-30/KC-45 would have all had the same issue with scrapping stealth aircraft). Refueling in turbulant air and weather cause the most scraps, although a Boom can scrap a receiver in smooth stable air, too. Boom Operators do account for scrapping too as do receiver pilots.
I don't see the scrapping issue as going away as long as we do Boom and Receptial refueling, there are to many variables, most of them are not under control of the Boom Operator or Receiver Pilots.
The fuel lost during disconnect is about 1 quart/1 liter, which is the capacity of the receptical before the poppet valvue,