SERVER-125400 introduced a fail fast option for setFCV when there are ongoing index builds in progress. Due to the async nature of index builds and when the user sees a response, this can cause the user to receive an OK for an index build and then receive BackgroundOperationInProgress when issuing a setFCV command immediately after (not concurrently).
A createIndex command returns to the user when the index build's promise is fulfilled. After this, the async index build thread still does some work, including completeAndLogOperation. This thread is the one marked as long running, meaning that even though to a user the index build looks complete, a subsequent setFCV can fail due to the clean up work still being done.