I have spent several hours searching and haven’t found anything specifically about this in Cubase except for someone else having a similar problem due to too many plugins in their folder, and therefore couldn’t find the right plugin. Or maybe if there are plugins that aren’t VST3 in the folder it causes a bug of some sort? The thread wasn’t at all clear. But I checked my plugins folder.
In my list of plugins, all the iZotope plugins imported automatically into the general folder. None of them have the /// that supposedly shows that they are VST 3 plugins. But they ARE VST 3 plugins!
I don’t have Neutron 3, but it seems you have the VST2 and the VST3 version of Neutron installed, and if I interpret you post correctly they both show up in the plugin menu. That means that they have different internal IDs, which is why Cubase treats them as different plugins and cannot see the presets.
In that case, it’s an oversight from izotope. Not much you can do there.