This still doesn't get you all the way, since you're ultimately trusting your chip manufacturer.

That it's an issue of trust is the reason that's not true. You know certain groups are highly-unlikely to work together on a backdoor that works same for all of them. There's also folks like Wirth's group at ETH that's unlikely to be backdooring things at all. So, the easiest route is to write your bootstrap phase is several languages that use tools from very different people and countries. You can trust it once they produce the same output. Use that output to bootstrap the rest. Also, do it on different hardware and OS's if concerned about that level. Make sure the CPU's were done at different fabs.

Aside from trust, the other reason people are doing this is for fun challenge of building things from ground up. They also are learning about interpreters, compilers, assembly, etc. The author of this work talked like he is doing it the way he is mainly for the challenge.

I think this is a very cool concept, but it doesn't seem to protect you from your environment. When you write the program in your editor, how do you know it's not inserting rogue code before it writes them to disk? When you run an assembly program stored on disk, how do you know the OS or even the hardware isn't patching it before it runs it?