I typed my method below before reading your full post on what works for me, but after reading your comment I think BIM 360 is just refusing your 3D views because you've basically setup the parent folder "Project Files" as your coordination space (I don't believe this is how you should do it), Model Coordination could just be refusing to show them. You should be selecting a folder, be it the "Shared" or a "Coordination/Clash" folder and setup a coordination space within that for clash detection.
I have never exported the default {3D} view when publishing, so try this method below and it should help:
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Each of the model files that are within the "ClashZone' coordination space you have created is exporting {3D} as their default published 3D view. (It doesn't have to be published with this view) You need to go to publish settings in Revit, choose the 3D views you want to include for clash detection.. NOTE: (BIM 360) uses clash detection by clashing view against view. Each model needs to have the same 3D View Section Box for the clashes you would like to perform, E.g. If it's focused on Building 1, each model needs a section box on Building 1 and you will need to publish that 3D View which focuses on Building 1 in the Publish Settings under <Manage> in Revit for each model. (Call the 3D views something like:
Building 1 _Structure
Building 1_Architecture)
etc.
Option 2 is to create a federated model and save it to it's own BIM 360 folder under project files so that it can have its own coordination space with all Revit links linked into this blank model. You can then create a 3D view for each discipline, so you only need to publish 1 model for when doing clash detection, plus this gives you the ability to setup the 3D views as required, instead of relying on other consultants to create 3D views and publishing.
To take it a step further, if doing option 1, you can disable clashes for certain views in the settings option under model coordination.
But I much prefer option 2 because it's much cleaner only being able to see the 3D Clash views I have published to BIM 360, due to it being in it's own unique coordination space.
Hope this helps, happy to chat more to elaborate my workflow.
P.S. It can take quite some time for these new views to pop up in model coordination. It wasn't instant once I republished.. Took hours.