An update from me as well.

For the end of June I had booked AP with AZ flight numbers, ATH-VCE. My gf was supposed to fly in on that ticket, while I was flying in (and returning) from work at AMS with KLM.

Outbound she received free checked bag. A bus gate in ATH, and a bus gate in VCE. No lounge invitation was offered.
Due to a severe food poisoning (guys, don't eat seafood at any touristic place like Venice!) we decided to give up on her returning to ATH and I booked her on my KLM flight using Flying Blue miles. The air one checkin desk didn't care to know about her not flying the last segment and pointed me to the ticket desk. After waiting in line for 45 (!!) minutes I gave up and left. So she flew with me back to AMS, and a couple days later back to ATH where she was expected for work.

The one segment she did fly with AP I tried to get credited with FB. It didn't happen automatically, so I asked at the flying blue desk at the crown lounge in AMS. After much calling of colleagues I was told that flying blue explicitly denies awarding miles for AP operated flights, and that the info on the web page is outdated. I didn't wanna leave it at that and told them the flights were bought at an higher price through AZ specifically due to the miles that the KLM website says would be credited. Since this was an early morning (6am or so) the main FB office was closed and she couldnt contact a supervisor. Guess I'm gonna try again. Out of principle I want that handful of miles now

So to summarize:
- with AZ flight number you get a free checked bag
- typical llc model: bus gates, BOB, huge queues everywhere
- FFP miles: to be seen, probably not

Oh, and probably totally off topic: Flying Blue award flights are great last minute. A one way VCE-AMS, a few hours before departure, was first offered to me for over 500 euro at the ticket desk in VCE. That same seat I was also able to get for 12.5K miles + 15 euro tax. Great value!