You do this once and your Engine is ready for packaging. Of course you still have to apply the Patch I will provide when I am finished or use the branch I will provide and/or try to get some parts merged into Epics main branch.
The script clones emscripten and emscripten-fastcomp and compiles them. After that it will get the node.js package and move all stuff that is necessary for UE4 into their folders. After this point UE4 will be ready to compile the HTML5 Platform. I used UnrealFrontend to package and run the HTML5 project.