If you're checking in with a partner you have to get their app to show the real mobile boarding pass. I.e. if you're flying from the US to AMS, even if it's on KL metal with a KL ticket under a KL number, check-in is handled by Delta and you have to get your boarding pass from the Delta app.
It used to be the same for AF/KL but they've wisened up to that now, it seems, and let each other's app show eachother's boarding passes (albeit in the style of the app used).