In the case of ACF installed in a theme, if a stand alone ACF plugin is installed then it will always be used. Plugins are loaded before the theme. There isn’t any 100% effective way to avoid conflicts with 2 versions of ACF that I know of. This is true of any plugin. If someone comes up with a solution, other than not including ACF in a them or plugin and requiring that it be installed separately I’d be interested in hearing it.
