Yeah, apparently Atomic still does that. They provide alternative version of psa-proftpd package for some reason, as well as some others. However I think I never saw malfunctions caused by this. Plesk usually works with Atomic quite well.
Since 11.5 it should be perfectly fine to use almost any third-party repository, as long as they provide packages with valid dependencies. Usually Plesk installation or upgrade won't start if this is not the case. However the safest way is to use only OS vendor repositories. The most popular third-party repositories that are used with Plesk on CentOS are Atomic and Remi.
Repositories are usually configured in /etc/yum.repos.d .