Flarum relies on modern web APIs for responsive design, history management, and other features. Some extensions might rely on intersection observers, geolocalization, and other HTML5 features.
These features might either not work as intended or be completely unavailable inside iframes due to the increasingly stricter security mesures introduced by browsers.
We do support using iframes inside of Flarum, a feature the MediaEmbed plugin relies upon for embedding video players and other websites in posts.
If you discover glaring issues with Flarum inside an iframe that are easy for us to fix, feel free to report them on GitHub. But I don't think we will be adding any extra code to work inside iframes anytime soon.
To come back to your situation, if you are embedding Flarum in an iframe it means you successfully installed Flarum in a subfolder or another domain.
Once you have that working, why do the extra work of setting up an iframe and linking to that iframe instead of directly linking to the domain where you installed Flarum? Just link to the actual URL where Flarum is hosted.