I wrote the blog you were referring to!
We can not expect the backend listener metrics to give you an accurate result as you expect in the aggregate report - (specially percentiles, avg etc)
BackEndListener basically gives the metrics over time. You should plot the graph using the data over time. If you try to use single stat metric of Grafana with that data , then you will see a complete mismatch.
In the blog - I was using the modified apache_core.jar library to get the results as you are actually expecting. However I stopped sharing (after jmeter 2.13, jmeter 3.0) the modified lib.