This happened to me. UA booked but flying J NZ metal. Well I was I'm their budget economy fare class. At first when I rang Air NZ they told me that I would only earn what UA had put me down as. So I earned about 30 sp. I complained about it on here months later, and people told me to fight it. Rang up Air NZ and they told me it was a mistake and actually, regardless of UAs fare class, I should have been credited with J SP earn. And so I went from earning 30 SP to 300 SP.
So yes, you will need to check so that you can ensure you get the SP that you are owed, and yes its Air NZ metal so counts towards elite.