I've answered my own question. Here's a good description of the theory behind the head bolts.
Bolt Engineering - Torque to yield and Torque/Angle Tighten (TTY & TAT) - Mickey's RV8 Site
The head bolts are torque-to-yield. They stretch out some when you torque them down. Because of that, they should not be re-torqued, and should be replaced when you do the gasket.
With graphite gaskets, when the aluminum head expands with heat, it compresses the gasket some. The MLS gasket doesn't compress much, so the TTY bolts stretch some (maybe they just expand with heat as well??) to account for the expanding aluminum head.
I'm trying new head bolts from a cheap head gasket set by Evergreen. I figure if they are made out of the same grade metal, which they appear to be, they will yield at the same torque and apply the same force at that point. I will update this post if they ever fail on me.