I have been reviewing about WordPress Flynt Theme a week ago.
I am going to develop a complex wordpress site by using Flynt. But I am not sure that Flynt will work without any doubt and has any conflict with famous Wordpress Plugins such as SEO plugins.
I'm one of the core contributors of Flynt. We are using Flynt for all our custom designed WordPress projects ourselves, may it be rather straight forward websites, or more complex ones.
As a general rule, we try to avoid using too many plugins in our projects to avoid compatibility and security issues. We're also making limited use of WYSIWYGs and shortcodes, but rely on custom fields with ACF Pro instead. Everything revolves around custom built components.
We're of course using popular plugins like Yoast SEO, Contact Form 7, and WP Super Cache. But Yoast will require ACF Content Analysis for Yoast SEO as a plugin for the backend to make things work. This will be similar for other plugins which are scanning the_content() to add functionality, as the component architecture is independent from the_content().
I'm sure Flynt will work like a charm for you if you love custom development, but you might run into issues if you're heavily relying on plugins to add frontend functionality.