It doesn't conflict with other configuration management systems. I've used openSUSE extensively with puppet and saltstack.
Many of SUSE's products use other configuration management systems as part of their toolchain, and SUSE are shipping SUSE Manager 3.0 with SaltStack, so their customers are expected to be able to use YaST alongside such a system
http://www.rubydoc.info/github/yast/yast-yast2/
http://yast-core.readthedocs.org/en/latest/
I am not trying to make you angry, but I think I put the finger right on the place where it hurts very much.
There is no clear documentation about what yast does or what it will not do - basically a blackbox. Maybe it will change apache config. Maybe not. Who knows.
Users know - YaST doesn't change stuff without telling you, that was the point I was trying to make earlier. Users of YaST no longer have to worry about it silently taking over config files, it either co-exists or doesn't do anything without telling the user with great big pop-up boxes first