Yes. The silicone varies. The red has problems, the black is the best and less sensitive to contaminants on the sealing surfaces but I've had good luck with the simple blue as long as you wipe everything down with alchohal to get everything clean. It has to be completely dry also or you will find places when you strip it down that it didn't stick.
The black as it cures actually pulls the pieces together.
As far as the guidance studs go, I find using four is to many for me and one on each side is enough.
That isn't a new idea though. If you have worked on Ford small block 289 series engines (260-302) you will find that when using the iron intake manifolds, the factory has used studs on those four positions since the early '60s.
I'm sure that Marlin is right on that, laying down the intake, especially a heavy one like the iron intake, you get much better results if you drop it on the exact correct spot to begin with without having to wiggle it around to align the bolts.