BIN is the best primer for knots, but that doesn't mean it is guaranteed the knot bleed will never come back. It's just the best thing to use.

I never like to use a water based primer on bare wood, as it tends to raise the grain. Further, most water based primers don't sand as well as an oil based product. On a new ceiling, if I had the possibility, I would prime all those boards with the BIN primer before they go up. It is always nice to prime the tongues because tongue and groove boards often shrink a little as it seasons, leaving a little bare wood showing. Spraying would be ideal. BIN flows out really well and often does not need any sanding at all. The thin, even coat of spraying also does not tighten the fit on the grooves, making insertion with the tongues difficult.