Um - I'm not so sure that is entirely correct. To my knowledge, WordPress core now *supports* protocol relative URLs with the wp_enqueue_script and wp_enqueue_style functions. But it doesn't force them. Whether they are used or not depends entirely on whether a protocol is provided with the URL that is given in the wp_enqueue_script or wp_enqueue_style function. These functions will simply take whatever URL is given to them (either starting with a protocol or without), and output that URL as-is.
This can be seen in the WordPress patch that provided this functionality via https://core.trac.wordpress.org/ticket/16560. The patch allows for URLs that start with either http, https, or just //.
Themes also can use either method. I'm using a child theme that runs on Genesis Framework, and my theme has a setting (checkbox) that lets me enable or disable protocol-relative URLs for the theme's own .css and .js scripts. If I uncheck this setting, the theme URLs all begin with http:// because my site is not running with SSL.
If your plugin could have a similar feature - just a checkbox to let me use one or the other - then it would allow for all possibilities. This will be fully compliant with WordPress core. :)
What do you think?