qa: update testStorageUpgrade data for what is not automatically upgraded
Some changes in the storage format are minor and applying them automatically would cost too much for big databases. Here, we apply them manually so that testStorageUpgrade will be able to compare dumps. We hope however that with improvements like https://jira.mariadb.org/browse/MDEV-12836 we'll be able to implement more migration steps and revert parts of this commit.
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