@Dave.
Thats not true. All VS operated flights are eligible for SkyMiles earning, regardless the booking method, if it is VS-marketed.
What I think you mean is that VS flights marketed as AF/KL are not eligible.
For example, VS001 (LHR-EWR) has the following codeshares:
(AF) 6750
(DL) 4380
(KL) 4818
(SQ) 2581
On the DL partner earnings site its clearly listed that KL-marketed flights are only earning miles if its SkyTeam-operated. However, on AF it is written that any AF-marketed flight earns, except a few exceptions, but VS is not listed among those. So if you fly VS-operated AF-marketed flight, and credit them to DL, and they don't give you the miles, you can refer to their website, because according to it, you shall receive them.
And otherwise, no matter where you book, if its VS-operated and marketed, you always get your DL miles.
VS recently started partnership with many many airlines, (BE,BA,TK,AZ,AF,KL,EI etc) to fill their longhaul routes. I always fly BUD-LHR (on BA), LHR-JFK (on VS). Its on the same ticket, issued by British Airways, but since they have no codeshare on VS, the transatlantic sector is marketed by VS. And I always earn miles for DL, and I can use the lounges (I am SkyMiles plat.). I can even ask the check-in agent to manually enter my Alaska MVP number to the BA-operated (and marketed) segment, and the Skymiles number to the VS-operated segment.