I can't foresee any problems. By default, ApisCP employs principle of least privilege meaning the web server runs as a different user than the account admin. There's a couple strategies to integrate with varying levels of security. Learning Mode will allow temporary write access and calculate the permission differences, creating a custom profile for the app. Other solution is to give the directory, or subset of directories, web server ownership. Lastly, you can make PHP-FPM behave like cPanel, Plesk, and others by changing the pool ownership to the account user (Web > PHP Pools > Change Owner) or on creation by setting apache,webuser to null/None/"". It's bad practice however. The rise of third-party security services from cPanel's backwoods architecture should be indication enough to avoid same-user ownership 🙂
Waiting on a developer license, and some free time, to go forward with integration notes. If you ever run into issues, do reach out to me either here, email, or whichever is most convenient.