I will assume that you are not coming to a stand still on track for your longest straight run. With that said for discussion sake, any deviation in the corner leading up to this straight can effect your results at the end of the straight.
Any trajectory deviation in the corner, any throttle deviation, any brake deviation, etc. will make comparing results interesting. How do you know if the set up change made the difference or maybe the deviation of the driving line was the real difference?
Add in barometer changes, wind changes, cloudy or sunny changes, temperature swings, and tire grip level changes, it adds more complexity to evaluating results.
With a dyno, you have less variables to worry about.
Neither method is without potential error. IMHO the dyno has the better repeatability.
As always, the stopwatch is the final word. Run whatever yields the quickest lap.