The fact that Envato doesn’t allow Unyson to be built-in premium themes is just that. You can’t “include it” by default in your package.
Absolutely no one stops you from asking users - in order to get the awesome experience - to activate it via TGM and check if plugin is active and only then start serving the advanced functionality.
As long as your theme functions perfectly as a blog theme without Unyson loaded and active as a plugin, no reviewer will ever comment on the issue. You can add custom settings and styling for whatever plugin you want in the world, just don’t make it mandatory in order for the theme to function properly with WP’s defaults. So, really, no need to panic.