The test waits for the primary to finish the index build, before immediately shutting down the secondary. If the secondary hasn't yet processed the "commitIndexBuild" oplog entry to prompts an fassert, then the node will exit cleanly. The test expects the node to crash.

Modify the test so that it does not try to shut down the secondary until it has processed the "commitIndexBuild" oplog entry.  IndexBuildTest.waitForIndexBuildToStop(secondaryDB) should be enough to fix the test.