What I'm reading is that the OP's worried that if it's obviously a Storable file not that they can modify it using vi but that they can (trivially) retrieve, diddle the contents, and restore. Compressing it and removing the gzip magic means they can't just blindly gunzip it, not to mention that file(1) probably won't correctly identify the file contents.

Again, it's not intended to be a fool-proof mechanism but another layer of (again trivial, minor, laughable) obfuscation. I'm presuming they're just trying to make the config file slightly more opaque than vanilla Storable blob to discourage random tinkering as a shortcut (e.g. "This is just a quick tweak . . . ah, file fooble.cfg says it's perl Storable(v0.7) data. *clickety* perl -MStorable -le '...' *wham wham* Oops." versus "Hrmm, file fooble.cfg just says data; guess I'd better just crank up fooble_configurator.").

That being said, the entire exercise is pretty silly and they'd probably be just as well off with explicit policy and threats of bodily harm (viz. "You can get more with a kind word and a two-by-four than you can with just a kind word." :)