In VCToolChain.cs (\Engine\Source\Programs\UnrealBuildTool\Windows\VCToolChain.cs) you can append additional compilation argument in AppendCLArguments_Global() or AppendCLArguments_CPP(), if it’s c++ specific arguments.
You can do that for every platform you need, (Linus, Mac, IOS, Android, etc) in their respective ToolChain file (LinuxToolChain.cs, for example).