don't worry about menu difference, that was me testing something for sure
about the folder structure, i would suggest checking the file that was responsible of generating those folders first, as long as i remember, the only time i change anything related to that is in chapter 2 when i decide to pull out the plugins folder form under graph editor one to sit under buzz folder itself and that is done in project settings, so, nothing related to the code generating empty folders is changed at all, just double check it, if you saw things flash from 012 to 013, it's possible that i changed something and i forgot to mention in video, call for it here and i will put the code in this forum for everyone but if you are talking about the extra plugins under the assets, check your project settings, looks like one or few projects are pushing their result into different folder, also, check the content of the plugins that is sitting under Assets folder, i think sometime in project i had this when i set the temp directory to be different than the publishing directory and both were in unity project asset structure.
In chapter 2, i set the temp directory to be the bin/Debug and bin/Release to get rid of those temp junk that vs produces during the build and not showing them up in unity at all