fix: Always apply status when merging or replacing

[rquitales]

The refactor to include Apply and ApplyWithPrune interface methods in Storage caused a regression where status is not always applied. This commit ensures that the status is always applied.

[k8s-ci-robot]

Hi @rquitales. Thanks for your PR.

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[Liujingfang1]

/ok-to-test

[Liujingfang1]

/lgtm
/approve

[k8s-ci-robot]

[APPROVALNOTIFIER] This PR is APPROVED

This pull-request has been approved by: Liujingfang1, rquitales

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