Your way all the files get copied and that is OK. Publishing
gives you the option of selecting just to update what has changed.
Another reason for publishing is that sometimes you need to put
something on the server that is outside the project. Your way would
trash that stuff and you would have to redo it. If your way works,
stick with it.
Merging is something you do as part of the set up. How can
others do it without access to RoboHelp?