Currently, if you configure SavepointSettings in the initial Configuration passed to StreamExecutionEnvironment it is not passed to the StreamGraphGenerator. Therefore a chain of calls will not apply these settings:
Configuration conf = new Configuration();
StreamExecutionEnvironment env = StreamExecutionEnvironment.getExecutionEnvironment(conf);
StreamGraph graph = env.getStreamGraph();
JobGraph jobGraph = graph.getJobGraph();
This makes the UnalignedCheckpointRescaleITCase not testing what it is supposed to test.