Trying to upload files to a folder shared from another account

As you found, app folders are incompatible with shared folders, meaning you can't share an app folder, put a shared folder inside an app folder or put an app folder in a shared folder. Instead, if you need to use the API with shared folders, you'll need to use "full Dropbox" permission, as opposed to the app folder permission. You can find more information about app permissions here.

Using full Dropbox access, you certainly should be able to programmatically access a shared folder in your connected account. A 'missing_scope' error indicates though just indicates that while the app is permitted to use that scope, the particular access token you're using to make the API call does not have that scope granted. Be aware that just adding a scope to your app via the App Console does not retroactively grant that scope to existing access tokens.

That being the case, to make any API calls that require that scope, you'll need to get a new access token with that scope.