Yes, I had flown with VL and my boarding pass only shows the VL flight number. I booked the ticket through LH and the route to TSR is only served by VL. The booking class was S for both flights, which would normally earn 500 Tier Miles with A3 on an LH flight.
Now that VL is a full member of Star Alliance, I thought that you should also be able to earn miles – unlike with Eurowings or Air Dolomiti.