We don't specifically "use" Let's Encrypt, the example install script just makes use of it. You don't have to use the script or Let's Encrypt (it just makes the setup quicker).
Like most web apps, you could probably deploy ITFlow behind a reverse proxy. This is mainly beyond the scope of ITFlow though, it's a web server/architecture decision.
The only thing I'd say you'd have to watch out for is to tell ITFlow to look at the forwarded header for IP logging (https://itflow.org/docs.php?doc=config-php - DEFINE("CONST_GET_IP_METHOD", "HTTP_X_FORWARDED_FOR");)