The tasks Perl is designed to do are different than the kinds of tasks PyPy is designed to do, so it is a bit of apples an oranges comparison.
PyPy starts to get its speed benefit when a task takes 1) longer than 3 seconds to run and 2) Is directly written in Python, not using libraries written in C.
Perl is designed to parse large files, do string parsing, and one off scripts. It being fast is nice, but it's not designed to be running large math heavy processing scripts to begin with. If a Perl script takes longer than a second to run, not including IO limitations and network limitations, it may not be the ideal tool for the job.
So while PyPy gets comparable to Perl speeds, Perl being fast is almost moot, because it's not designed to be used that way to begin with.
