one nice thing about this approach is that you can specify how different file handles get flushed.

I agree that using IO::Handle methods is nicer but just the approach with $| allows for the same granularity.

It is not the case that setting $| to true turns on autoflushing for all file-handles. It only affects the file-handle that had been selected (or STDOUT when none had been explicitely selected).

see "perldoc -f select"