Autocommand vs ftplugin

There is something I'm not understanding about this: if I write this
in my .vimrc file

au BufNewFile,BufRead *.php let php_folding=1 | set foldlevel=1

then php folding works fine, but if I put this two lines in
ftplugin/php.vim or after/ftplugin/php.vim

set foldlevel=1
let php_folding=1

then the folding doesn't work. What's the actual difference between
the two methods?

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