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.