It's an interesting coincidence that this question was asked, because just yesterday I was wondering the same thing about an executable I created about a year ago with perlapp, and since then lost the source code for.  After googling for a short while, I was directed back to Perlmonks, where I found this node.

Just for fun (and being just a wee bit lazy to dig into the executable), I thought I'd try for a slightly different solution.  So I wrote a Perl script which would:

1. Change to the temp directory holding the uncompressed files.
2. Prompt the user to change the priority of the Perl process (to "High".  I later tried "Realtime" for fun, but that turned out to be a mistake, as I had thought).
3. Prompt the user to run the executable created by perlapp.
4. At this point, I would manually change the priority of the application to Low.
5. The Perl script would continuously look for files as they were unpacked from the executable, and save their contents.

I'm sorry to say this yielded no success for me; the Perl script was unable to detect any files prior to their removal, despite the application running at an extremely low priority.

I don't know if this helps with the particular question of perl2exe, as I have no direct knowledge of that tool.  But if the mechanics of perl2exe are at all the same, perhaps a similar script would do a better job with intercepting the sourcefile while it's being extracted.