Wow, I have redesigned the project to IWYU as in this article, and now compiles realy fast 5-15 seconds!
Compilation from the studio and the editor works and there is no conflict.
https://docs.unrealengine.com/latest/INT/Programming/UnrealBuildSystem/IWYUReferenceGuide/index.html
in a nutshell:
1_ Turn on the mode in .Build.cs
PCHUsage = PCHUsageMode.UseExplicitOrSharedPCHs;
2_ *.cpp files include their matching *.h files first.
3_ Remove YourProject.h from all sources, now heavy Engine.h does not participate in their compilation
4_ Optional сhange the #include “Engine.h” to “EngineMinimal.h” in YourProject.h
5_ Profit!
The compilation is really fast, thank you epic!