Your method of multiple formats in one zip is the best way to go. Some people have issues with that because of the upload issues. I tried zipping up my Jupiter 2 project with multiple formats in one zip but the file was so large it constantly timed out on me. Hence the mutiple uploads. Do what works for you and don't worry about other people's issues. They're their issues not yours.

It is a miracle that curiosity survives formal education. - Albert Einstein