Can someone explain how this is valuable for security or what this means for the justice department?

It opens up parts of the system to scrutiny by security researchers and developers that previously were not. The idea is that they would be able to crowdsource security research, as well as slightly improve performance by not having the overhead of encrypting non-critical data. In no way does this affect user data.

It means Apple is bowing to the demands made by the DOJ.

I think it means Apple considers their secure enclave "secure"

User data is still encrypted.

I'm not so sure. Wouldn't leaving the bootloader/root filesystem unencrypted make the device more vulnerable to physical tampering by a non-Apple party that could compromise user data?

I'm assuming that these things were previously encrypted/signed with a key that only Apple controls. I could be wrong.

Everything is signed and most likely the parts that do the checking will stay encrypted.

It's a beta not designed for production use, it is entirely possible these are temporary steps taken to assist pre-release debugging and development troubleshooting. I'm not saying that's the case but I wouldn't rule it out.

In other words, testing iOS 10 found battery last went from 3 hours to 5 hours! I have no idea if it's related to not having obscurity.

Does this also help find new jailbreak opportunities?

It sounds like Apple is abandoning the idea of security by obscurity, which is a very dubious stake to have if you ask me.

Also this probably does a lot in reducing the overall burden of government request. If you have nation states demanding your source code, why not just open source it.