Hello Bonorose,
I think this part of your original error log looks similar to UE-36717 error log I saw:
LogPlayLevel: HTML5Platform.Package: Setting Emscripten SDK for packaging..
LogPlayLevel: Program.Main: ERROR: AutomationTool terminated with exception: System.IO.FileNotFoundException: Could not find file 'D:\Epic Games\4.11\Engine\Intermediate\Build\HTML5\.emscripten'.
Do you happen to have HOME environment variable on your PC? That seems to make Html5 packaging fail(in 4.11 and later), so if you have HOME env var, could you test if deleting the env var make a difference?