To get the desktop plugins to work i found i needed to copy the plugins provided by flutter specifically for desktop into my project. I also updated the yaml configuration.
Source for plugins.
https://github.com/google/flutter-desktop-embedding/tree/master/plugins/flutter_plugins/path_provider_fde
Note: i believe these plugins will change and eventually become part of the default package installed.
Things like getApplicationDocumentsDirectory are provided by Flutter, but the windows implementation is currently in development, so you have to provide the additional plugins which have the windows/mac/linux implementation. Which can be found on the flutter desktop pages. (link above)
Below is what my folder looks like.

And my pubspec.yaml
dependencies:
logger: ^0.9.1
dependencies:
auto_size_text: ^2.1.0
draggable_scrollbar: ^0.0.4
provider: ^4.0.1
flutter:
sdk: flutter
file_chooser:
git:
url: git://github.com/google/flutter-desktop-embedding.git
path: plugins/file_chooser
ref: 4ee135c
path_provider: ^1.5.1
path_provider_macos: ^0.0.1
path_provider_fde:
path: ./plugins/flutter_plugins/path_provider_fde
window_size:
path: ./plugins/window_size
url_launcher: ^5.4.0
url_launcher_fde:
path: ./plugins/flutter_plugins/url_launcher_fde