But any new music I add won't have the proper tree stucture without me creating it manually - is that what you are saying?

Something like that.

The current player software doesn't have any way of selecting artists and albums from the Soup views from the front panel. You can only select playlists.

So if you drop a track into a Soup view, it's not going to show up on your playlists menu unless you specifically create a playlist and put it in that playlist.

BUT...

If you drag a windows folder of tracks and drop it onto the playlists view in Emplode, it will automatically create a playlist that's the same name as the folder you dropped.

It seems that your confusion is merely with your drop destination. If you drop onto the playlists views, it works as it always did. If you drop onto Soup views, it behaves differently.