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.