i also used bathroom grade clear silicone last time and many times and it works fine.
I did use the permatex #2 once and noticed the stuff never completely hardens. I would think this is the best stuff and we all should be using that.
I suspect that #2 Permatex was what the GM guys had in mind when they wrote the specs the first time. That info is lost in the history at GM. Now there are so many sealers, thread lockers, and just plain goo out there it's tough to decide. I use Locktite Thread sealant with teflon. Seems to work fine. Stays pliable, and is a PITA to clean up.
I also read something years ago -- I torque SB head bolts to 70 for all but the row of short bolts under the manifold- those go to 65. Reason is that the short bolts don't stretch as much... But that's with stock iron heads too. Aluminum I'd go with the mfr's specs. And most of the alumunim heads have a deck that's 1/2 to 3/4 thick.