As a rule, we don’t offer support for hacking Backlight’s core modules. Our expectation is that users should implement their coded customizations via the backlight/custom folder, and using the provided extensibility features (PHPlugins, custom stylesheets, etc.).
pangolin-page loads the Fancybox script for every type of page, with minimal customization for Backlight. And so, if you want to create a custom Fancybox implementation, then do not hack Backlight’s core modules, and do not use pangolin-album (which heavily customizes Fancybox for Backlight).
Instead, use Galleria or Theater as a base, use PHPlugins to completely replace the image loop, and then also use PHPlugins to initialize your own Fancybox configuration. There’s already an example, “Create a custom image loop for albums”, in the PHPlugins sample file.