SERVER-39074 is complete, all operations default to enforcing prepare conflicts. Unfortunately, due to the problem described in SERVER-40176, this means that occasionally, prepare conflicts can be encountered when otherwise valid cursor seeks are adjacent to prepared records.
This is only problematic for "applyOps" entries because inserts ops are converted to upserts. This means a query on a nonexistent record, which uses search_near, can land on an adjacent record that is part of a prepared transaction, introducing a prepare conflict that would not have happened on a primary.
Transaction use "applyOps", but all inserts as part of transactions should be able to be applied as inserts instead of upserts. This also means prepare conflicts can be enforced during secondary batch application.