The problem is you cannot upload a .exe filt to the Windows Store you need for example a .xsix file. To build a .xsix file it is very easy:
You build your app with Flutter for Windows and after this step you can use the xsix package to build a xsix file for the Windows Store. You find the documentation for the package here: https://pub.dev/documentation/msix/latest/
Add this package to the dev_dependencies:
dev_dependencies:
flutter_test:
sdk: flutter
msix: ^2.1.1
And then use these comments:
flutter clean
flutter build windows
flutter pub run msix:create --store
After this steps you get the msix file for uploading to the Windows Store.