JMeter have three basic measurements it captures per request:
Elapsed Time (which is overall timespan from the point when it just starts sending request to the last bit received)
Latency (which starts the same point in time and ends when server starts responding)
And Connect time (which is included in latency and is basically the time for handshakes with server, including SSL/TLS negotiations)
So if you set a data writer among your listeners (e.g SimpleDataWriter, although AggregateReport & SummaryReport can do it as well), you'll see these metrics in your data file (while standard listeners/visualisers/aggregators stuck to elapsed time only).
But mind that these metrics doesn't include response rendering, and especially any code to be executed by browser.
JMeter just doesn't do it at all: obviously, it measures just the combined performance of Server + Network, skipping everything on the client side (except for bare necessities, like protocol negotiations).
That might explain the difference you've experienced.
As well as the difference between logged server processing times & the response times measured by JMeter: server just doesn't count what the network brings in.
PS And you don't have to sit and click on stopwatch with your browser: modern ones have a Dev Tools capable of showing you the precision timings divided by stages. E.g., just call Ctrl+Shift+I in Chrome, switch to network tab & behold the timings right there as you doing your requests.
