Well, that is just how names work. Google was the first to register google.com, and now you "trust" that google.com belongs to them.
The blockchain is no different, except that it gives you even more reason to trust that the ownership hasn't changed.
> the only room for injection is at registry time (modulus the 30 min window as discussed in the links), rather than simply mitm the connection at the time of first use?
Right, and registry time isn't really an attack. It's a legitimate registry.
Someone could register google.ninja right now, but you wouldn't trust it because Google has established the .com (via word of mouth and links, essentially) as the de-facto website.
> And bootstrapping trust into the blockchain is basicially by trusting the ca-cert/github documentation?
Sorry, not sure I understand what you're asking there.