Fix RaftCluster boostrap being based on v3 store while apply is based on v2 store. #16655
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Migration off v2 store was unfinished during v3.5 development #12914 leaving RaftCluster broken, half migrated. This was found in v3.5 and fixed in #13348, however this is was not patched on main branch.
This PR makes v3.6 RaftCluster consistent with v3.5 so we can cleanly migrate off v2 store.