Preventing node 0 from running for election for 5 seconds before doing a reconfig is not enough time to ensure node 1 is elected. We also do not do any waitForState on node 1 to make sure it is actually primary.
To address this we should increase the timeout in the stepdown before node 0 is able to become primary and actually wait for node 1 to become primary before doing the reconfig. We can then use a replSetFreeze: 0 to reset the election timeout on node 0. Using ReplSetTest::stepUp could fix this. We also should make sure node 1 is actually elected primary before doing the reconfig. Asserting that node 0 is secondary is not enough.