The flight is sold as Virgin but operated by US, i.e. it's a codeshare flight not operated by Virgin but by Virgin's codeshare partner. The note says mileage for N fares on Virgin codeshares is per the operating carrier's agreement with US. So a US operated flight sold as Virgin would give miles based on US' agreement with US or 100%.

I think where things get confused is that US doesn't have an agreement with US. I would read the note as saying that a flight sold as a US codeshare partner's flight (Virgin in this case) but operated by a third carrier (XYZ Airlines) gives miles based on the third carrier's agreement with US. Otherwise every US flight sold as another carrier's flight number would earn 100% mileage even though the codeshare partner might pay 50% or even 0%.

Jim