I've gotten miles for each of the half-dozen or so interviews I've flown to. It's never been an issue. The one time I forgot about it, I actually got asked if I had an FF card by the airline staff at check-in.

The companies couldn't have cared less. They just booked the tix and told me which flight to be on. After that, they never asked about them again.

They even flew me in C once!