Yes, the default collection places items in their default locations. That way you will always have a collection with everything set to their defaults. You can however make another collection that is a full copy of the default collection and modify that as you see fit.
Actually the PlugIn Manager works perfectly (although a new collection won’t automatically show plugins added AFTER the collection was created).
The main thing is that, after you create your new collection and organize it how you like, just don’t switch back to the default list in the Plug In Manager. The collection that is showing in the plug-in Manager when you close it, is the one that will show when you click on “Add Instrument”.
Well that’s actually the way it should work. When you add a new plug-in, it gets added to the default collection because that’s where you want to be able to find every plug-in. But Cubase shouldn’t add plugs to user created collections since there is no way for it to know A) if you even want it in that collection, and B) where to put it in the collection’s folder structure. For example, say you have 3 different collections one each for tracking, mixing & mastering. If you add a new plug, there is no way for Cubase to know if it should go in any or all of those collections.
FYI - you can put the same plug-in into a collection multiple times. I’ve got a collection with folders for each type, EQ, reverb, modulation etc. But I will put my go-to plugs in both the folder and also at the top level so I don’t have to navigate to find them.