Changing BuildConfiguration(.xml) in 4.16

Generally you should only need to modify things in the Build.cs file if you need them on a per-project or per-module basis. Otherwise use the following locations of BuildConfiguration.xml:

Engine/Saved/UnrealBuildTool - For a specific engine version.

Documents/Unreal Engine/UnrealBuildTool - For all installed engine versions.

I just have the following at the latter location, for example:

<?xml version="1.0" encoding="utf-8" ?>
<Configuration xmlns="https://www.unrealengine.com/BuildConfiguration">
	<BuildConfiguration>
		<bShadowVariableErrors>true</bShadowVariableErrors>
		<ProcessorCountMultiplier>2</ProcessorCountMultiplier>
	</BuildConfiguration>
</Configuration>

The fact they seem to have removed the default one in 4.16 shouldn’t matter, the defaults are still no doubt defined somewhere, so you can just add to the empty shell in Engine/Saved/UnrealBuildTool, or add a similar one in the documents folder if you want it to persist for future engine installs. Anything not specified will just be inherited.