[GR-70846] Ensure core types can be treated as closed

[graalvmbot]

Core types ideally should all be in the initial layer and should also be treated as closed.

There are some exceptions as some types are currently duplicated across layers.

This PR adds checks to ensure those assumptions.

• Except duplicated types, core types cannot be reachable only in an extension layer.
• Core types cannot have a new reachable subtype in an extension layer.
• Core types cannot be instantiated only in an extension layer.