I quote @bcimini 's nice explanation:
IdentifyPrimaryObjects is actually a collection of smaller functions, like smooth, resize (to speed up), watershed (to declump), filling holes etc…
In 3D pipeline, you would see each of these functions is executed in an individual module, whereas in 2D you can just use IdentifyPrimaryObjects and all that will be executed.
So although we say IdentifyPrimaryObjects is not yet supported for 3D, you can effectively do it by building a series of modules as seen in the example Anne linked.
Hope that helps.