In our UE4 Source build we have made specific changes to the engine needed for certain features, or to allow for compatibility.

One Example is the Niagara particles – to fix compatibility we have applied a fix to our UE4 Source, but we cannot do this to the plugin, so we are waiting on Unreal to pull our change. Another example is Altitude lighting –  Unreal did not support all the features that were required for this, so we had to implement them in our source build. 

There should be no performance benefits, just additional features and compatibility where it could not be done through the plugin.