Who says you have to upload your code directly to the deployment directory? Upload files, switch symlink. Done. You are talking about a deployment technique that has nothing to do with PHP.
Nah, I am speaking about the general/majority culture of how it is done in PHP.
Do you not see the comments in this specific thread? The guy a bit higher up the chain thinks my issue is with "FTP vs SFTP", rather than "the version of the files at a particular moment in time".
He doesn't even understand why a partial view of the files could be an issue.
And the general sentiment in PHP is that "you can change any file separately, by editing in online on the server - and that is a good thing".