Ok, so I've been doing these tests in the background of my regular work and I think I finally figured out how this is supposed to work. Really disappointing that there are not better explanations online.
1-Create a model just for coordination, place it in a new folder. Mark this folder as a Clash Coordination Space. Link all other models into this coordination model. Turn off all relevant worksets from the link, ensure phase filter have the same name and properties in all linked files. Synch all phases between linked models.
2-Create an axonometric view for each level in Revit. This is actually more annoying and hard than it should be because section boxes do not snap to anything in Revit. To get consistent results, I used the "Align to 2D view" method, which is already one of my favorite ways to make 3d views.
At first, I made a plan view for each level and gave it the following View Range properties:
Top = level above, offset = 0
Bottom = Associated level, Offset = 0
View Depth = Associated level, Offset = 0
Then I went in the 3d view, right clicked the navigation cube and select "Orient to View > Floor Plan > select this floor plan"
That did not work well. It basically seems to give it an offset and not truly cut at the exact level. For example, I would still see a sliver of all walls that are on the level above. To fix this, I adjusted the properties of the plan:
Top = level above, offset = -5
Bottom = Associated level, Offset = -5
View Depth = Associated level, Offset = -5
Than I redid the "Orient to View > Floor Plan > select this floor plan" operation. This fixed the imprecise cutting of the section boxes in 3D. Basically, there is a lot of improvement required in this workflow if you expect us to get accurate and reproducible 3D section boxes in Revit, like allowing us to snap our section boxes, making the "Align to 2D view actually accurate to the original view" and letting users scroll through the list of 2D (it's a super long list sometimes and navigating it can be extremely frustrating since here is no scroll bar, just an arrow you have to hold to go down the list)
2-Once you have a perfect 3D view for each floor, duplicate for each and isolate one of the linked models on each floor. I basically ended up with the following lists:
Clash-1-All
Clash-1-ARCH
Clash-1-ELECT
Clash-1-FIRE
Clash-1-MECH
Clash-1-PLUMB
Clash-1-SPRINKLER
Clash-1-STRUCT
Clash-2-All
... etc, on and on
Add all these views to a published Set of views. Synchronize the model and publish these views to the cloud. It will take many hours to be ready on BIM 360, especially since it will not conduct clashes between all these views.
When it is processed, go to your BIM 360 project, go to "Model Coordination" and "Models".
Start creating your views. To create view "1-ARCH-MECH" that will compare both architectural and mechanical, select the two related models "Clash-1-ARCH" and "Clash-1-MECH" from the list of models on the "Models" page, then click "View" at the top. This will load both models. Once it is done, select "Save view" and name the view "1-ARCH-MECH". Make this view public, not private. Doing this for each view takes a really long time and seems like it could be automated...
Do this for all views.
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I will keep playing and updating this if I can figure out more about the workflow. In the meantime, I think this can be a good guide as the "missing manual" to how this actually works. Hope this is helpful.
The workflow is quite slow and imperfect. Will hopefully advise about all the shortcoming and tips I can find when I am done testing.