[TRACKING] Assess kustomize patch targets

### Summary / Objective

It seems that some patches are being targeted too broadly.

Targeting too broadly could cause unintended side-effects (see #276) and lead to misconfigs.

We should assess if the current kustomize patch targets could be narrowed to avoid such issues.

### Checklist / Sub-tasks

- [ ] Narrow the scope of kustomize patch targets to avoid side-effects
- [ ] Add tests to ensure configuration in manifests is sane

### Design Documents & References

_No response_

### Target Milestone / Release

_No response_

Start by locating the current kustomize patch targets and the manifests they modify; the issue does not name specific files or tests. Compare the target scope with the side effects described in #276, then add coverage that verifies the resulting manifest configuration is sane. Done means patch targets are narrowed and the manifest checks pass.

Written by the indexing model from the issue text.