that is simply not true
I have several installs in folders and subdomains and do not have to do any of that
I think your problem may be the owner/group for the /wp-content has changed from primary ftp user being the owner to the web server being the owner
Doesn't work that way for me. I'm the sysadmin for my server, and the entire content tree of the web server is owned by my username. All blog folders are owned by me. The blog folders' wp-content folders are owned by me. But I can't update any of the blogs using the auto tools without getting the error message that bernatagullo mentioned before.
I've done a series of tests. If the home folder of the ftp user is not the blog folder itself, then the auto-install fails. Every time. If you change the home folder of the ftp user to the blog folder, it works. Every time.
So what do you do if you have several blogs, all contained in separate folders inside the web folder? You can't use a single ftp user, unless you change his home folder to the desired blog folder every time you want to update it. Or you can create separate users, each of whose home folders are the separate blog folders, and then execute the ftp update using the appropriate username and password.