I'm using an old version of emacs (20.4) and it has a variable called cperl-under-as-char which I can Customize. It's set to 't' for me (by default I think, since I don't remember ever changing this) and everything seems to be working. Type "M-x apropos cperl" and look around some. FWIW the docs for cperl-fix-line-spacing don't mention anything about fixing spacing for underscore, but they are pretty sparce.