Hi, if you have full source code you can just debug UnrealBuildTool with the following command line (right click on UnrealBuildTool project → properties → Debug → Start Options) set in Visual Studio:
TargetName Platform Configuration
So assuming your game editor target name is MyGameEditor:
MyGameEditor Win64 Debug
Then just set UnrealBuildTool as your startup project in VS and Debug. All breakpoints set in you build.cs file should just work.