Cleanup outdated usage for functions in upgrade test

[JeromeJu]

Changes

This commit cleans up the outdated usage of apply_resources function that has been used to test yamls which had been refactored for e2e-commons script in the history.

It does not block the upgrade test from running as a CRON but could cause confusion as mentioned at #5193 (comment).

/kind cleanup

Submitter Checklist

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• Has Docs if any changes are user facing, including updates to minimum requirements e.g. Kubernetes version bumps
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Release Notes

NONE

[Yongxuanzhang]

/lgtm

[tekton-robot]

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