Hey Hoss,
Great to see you here 
!
Thanks for your questions, we give these concepts for granted but we should definitely clarify them in our docs!
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currently, the only connector that upon receiving takes care of updating/deleting previously received objects and geometry is the Revit one. In Rhino, AutoCAD etc the newly received geometry is instead added to a new Layer. We thought this to be the most intuitive way of handling updates, but we’d be happy to hear if instead you’d like a different behaviour.
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we have borrowed many ideas from git, but our version control systems behave a bit differently => if only one of your three boxes has changed you should still send them all (and actually if you have created a filter by layer, for instance, that will happen automatically). What happens in the background is that Specke will realize only 1 of those 3 boxes is new and in our database, only the new one will be stored. This is why you should see commits more like snapshots in time of your model rather than diffs.
Hope it makes sense!