Hi Rama,
the issue is when you Rebuild your project (the “re-” part is the culprit), the engines editor target gets cleaned and rebuild along with the games object and exe files. So automatic cleaning of just the games project isnt sensible.
Building the game project (without “re-” 
) is working just fine, as you point out in your tutorial and as your answer.
So if something goes wrong with building, as with inside’s build, he has to clean it manually. Not exactly difficult but not a great workflow. F.e. my computer isnt the fastest, if I have to rebuild Im bound to wait ages.
PS saw your edit. I gonna try if the command “Build only project” does it.