Config overrides should be based on merging the user config, not the resolved

[schaable]

The current behavior: config overrides are resolved first and then merged into the network config. This approach can be hard to reason about, potentially confusing for users, and can lead to issues when resolving fields that depend on one another.

Proposed solution: store the user config in the HRE (similar to v2), merge the overrides into the user config, and then re-resolve it. This simplifies the code and also ensures proper resolution of interdependent fields.