One of the major pieces of the Chrome DevTools Performance panel's instrumentation is the V8 Sampling Profiler, which provides the data about what JavaScript callstacks are active. That's exactly what builds the JavaScript parts of the flame chart.
The V8 Profiler has some startup cost. It's essentially gathering data about all the current scripts on the page. This startup cost is what's labeled as "Profiling Overhead".
That cost won't exist unless you're profiling, so it doesn't affect real users. :)
Source: I work on DevTools and added this particular event to the UI.