It is any possibility to override /com_virtuemart/assets/js/facebox.js, i tried with /templates/ja_events/html/com_virtuemart/assets/js/facebox.js but that not work...
vm is moving to fancybox rather than facebox in the next release by the looks of things.
Regarding ja-fancybox vs Vm fancybox
There will probably be differences and a straight overlay is unlikely to work