For starters, $|=1; in the Perl program won't affect any buffering strace might do on its output. The pipe to which strace writes a completely independent file handle from the terminal (or whatever) the Perl script writes to. Furthermore, a variable in one process won't affect a library in a different process.

Secondly, if strace doesn't buffer what it sends to its STDERR, the output is not going to magically buffer itself if redirected.

Unfortunately, there's no way to control whether another application buffers its output or not (unless it specifically gives you the means of doing so, of course).