Various refactorings for TransactionManager

Gitaly's write-ahead log will soon gain support for logging objects in pack files. To make that MR a bit smaller, this MR performs various smaller changes that are required ultimately by the pack file logging MR. The changes consist mostly of refactorings and test setup improvements.

Part of #4790 (closed)

Depends on !5612 (merged) and !5611 (merged)