Not sure. For example, my entire Cart page is in Elementor and because I’m using a Woocommerce shortcode [woocommerce_cart] I managed to change font, button color in Appearance > Customize with Generatepress pro controls. I will have a chat with Elementor as well.
If theres particular customizer settings that aren’t working then i would assume Elementor is overriding them or using different markup to the theme. Let us know what they have to say and if there is anything particular you get stuck on, there maybe some CSS we can throw at it.