Yes, as long as all of the controllers are on the same code, the config will be pushed down.
All of the next generation firewall features (AppRF 2.0) can be configured on the legacy master but the actual feature sets will only apply where traffic is terminated (locals). Keep that in mind if you're planning on any fail over to the master. For example, while DPI policies can be configured on the 3200, those policies will not be applied if APs fail over to that controller.
The latest 6.3 build or 6.4.0.3 should be done.