PhpStorm saving with Linux line ending on Windows
You can safely use \n line ending for .php and most of other files as well -- PHP on Windows will read such files just fine.
To set default line ending for all new files: go to Settings/Preferences | Editor | Code Style and change Line separator (for new files) option to the desired style (e.g. Unix and OS X (\n)).
To change line ending for a particular existing file: open the file and either change it via appropriate section in Status Bar .. or via File | File Properties | Line Separators
P.S.
If you do have EditorConfig plugin installed and enabled ... you might also configure this via .editorconfig file -- there you may specify what line ending to use (this can be done on per file extension level .. so it's more flexible than PhpStorm's own setting).
This will also work in another editor/IDE that supports such file.