The team is now working on the WordPress Interactivity API. This unblocks the same UX Frontity framework enabled but directly in WordPress Core, fully compatible with the new Site Editor.
But I don’t think that’s the best idea anymore, because it could compromise security. If people do the build in the same server, the server bundle will be exposed in the /wp-content/frontity/build/server.js file, accessible from the Internet, and could leak a secret if people don’t use env variables.
It would even be possible to install WP (and plugins/themes) with NPM (or actually Composer, but can be linked), which in some situations is a security requirement as well (manually settings updates).
I can’t think of any reason why Frontity in the root would cause permission problems, just as much as WordPress in the root would.
However a proper setup where both are separated completely, with their own apache/nginx paths, would be the most preferred method. Although running WP in a subdirectory can offer a decent amount of security when done right.