Resolve why rust-tuf diverges in a few places from the TUF spec

[erickt]

There are a few places where rust-tuf diverges from the TUF-1.0.5 spec, like #113. This is a tracking ticket to label all these locations in code, and resolve why we've diverged, and whether or not we should re-converge with the spec, or try to fix the spec to match our implementation.