Here's a short update with my experience, as of today, having my second name on the ticket and all my three names on passport as well as Air France freq flier account. In this case it is not possible to connect my booking with my freq flier account.
The advice from the Flying blue staff is "It is of importance to not have encounter problems at airports, which means that your name needs to match your passport. Please make sure that your tickets are booked via the name that matches your Flying Blue account and official passport. "
In other words what they say is that I should have all 3 names on the ticket and of course they charge to make any changes to the ticket.
