"To instrument" means "to measure", but to me at least with a connotation of having points where to hook things to.
I didn't even recognize the original comment as mine, and I'm not really sure what I meant back then. I guess that my reply stemmed from a reading of perl510delta or the changelog of the profiler.
But yes, I think I suggested back then that the extra granularity/detail resulted in attributing 17 ms to a BEGIN call that was not separately accounted for in 5.8.8. I guess the time spent in the BEGIN block was added to the time spent in the main program.