I have not been able to duplicate any issues with it together with Minify. mfunc code can only be used with theme template files, post/page content or widget areas. That is displayed content that is cached by the Page Cache.
Code within mfunc does not know anything outside of the mfunc tags. So it can't call any functions, set variables etc in the template files themselves outside of the mfunc tags.
You can only call functions defined in plugins and also WP functions if you enable late init.