It sounds to me like the requirement here is to intercept the USB data, Wireshark-style, so that the data is being read by the Perl program while it is also being read by the proprietary software.

I think that it is safe to say that some “OS-specific privileged-mode high magick” will be required in order to do that.   Or maybe just a piece of wire.   If the data is simply coming in as a serial data stream, and it is now being sent using USB just because those connectors require a lot fewer wires (i.e. no command-and-control data going the other way), then perhaps you could electrically split the wire using some kind of a pigtail without running into impedance or voltage-drop problems.