The code is structured today such that one could call add() to add a node to the ReplSetTest internal state tracking, and then reInitiate() to reconfigure the replica set with the new node. However, reInitiate() loses custom config options that were originally used when constructing the ReplSetTest.

It looks like this is caused by the method constructing the new config document purely based on membership (via getReplSetConfig) and not based on the current settings (via getReplSetConfigFromNode):

https://github.com/mongodb/mongo/blob/r3.3.5/src/mongo/shell/replsettest.js#L629

this.reInitiate = function() {
    var config = this.getReplSetConfig();
    var newVersion = this.getReplSetConfigFromNode().version + 1;