Questions about a loki upgrade from helm chart v2.x to v3.2.1

I am trying to upgrade a single binary loki server installed by helm chart v2.x to the new v3.2.1
There are some questions that popped up:
Currently we are using filesystem storage with table_manager deletes enabled. But in the new helm chart there is no configuration for table_manager anymore. Is it done so deliberate in order to promote using the compactor? Does the compactor work ok with filesystem storage as there is this in the docs:

Retention through the Table Manager is achieved by relying on the object store TTL feature, and will work for both boltdb-shipper store and chunk/index store. However retention through the Compactor is supported only with the boltdb-shipper store.

As I look at the data directory - the logs are in the chunk directory. Currently the table manager is working fine.
2. In the current configuration the schema is as follows:

  - from: "2020-10-24"
      period: 24h
      prefix: index_
    object_store: filesystem
    schema: v11
    store: boltdb-shipper

But in the new one it is v12 with different prefix: loki_index

Is it safe to upgrade the version and to change the prefix?