I assumed $mod->VERSION() was well behaved and hoped it would handle some weird new practices that don't appear to set $Module::Name::VERSION. But it not coping doesn't really surprise me. I'll use it and detect failure and fall back to just copying the $VERSION global.
Though I don't see how this problem could be to blame for your "Not used?" result. As I mentioned above, that line only means "No exports used". If your code doesn't mention any of the *_NODE constants(?) that XML::Tidy exports, then that is the expected / desired result (and the recommended empty parens in "use XML::Tidy();" are recommended to document that no exports are being used).