I think the discussion about Activities and Virtual Desktop should take place in another thread. But to design the "plasmoid manager", some clarification is needed. Currently, virtual desktops and activities are two separate and orthogonal concepts. VDs don't depend on the activity like on the graph you made rumangerst. You cannot set a different number of VD by activity for instance. You can make a window appear on all activities and only on VD3, or only on activity "Work" and on all VDs. If you move a window on VD2 from activity A to activity B, it will stay on VD2 on activity B. So the two things are completely independent.

At least on Plasma 4, you cannot technically put different plasmoids on virtual desktops. The setting allowing you to do that actually uses a trick : it sets a different activity for each virtual desktop. And at least when I was experimenting with Activities (I stopped using them as I don't find them useful with their current possibilities and my needs), it was not recommended to use this setting (in part because it blurs the line between activities and virtual desktops, which are different concepts).

So for the "plasmoid manager", you need only to consider different activities, not desktops. Both mockups are really nice btw !