I don't have a problem with using black hi-temp silicone sealer in the intake manifold area. Of course, I always use a PCV valve to keep crankcase pressure down.

Some intake manifold gasket kits are 4-piece. One pair for the heads, and one pair for the engine block front and rear rails. On those, I just drop the gaskets in place, then put 4 dabs of black silicone at the corners where the gaskets meet.

The manifold kit on my new crate moter had only two gaskets - for the heads. The front and rear block rails were sealed with a bead of black silicone.

I've never had either method fail - as long as I used good gaskets, and the mating surfaces were not warped.