On second thought, add-ons originally not in the WE should add their menu items to the menu defined in their code — like a default menu position. For example, PolyCount installs its menu item in the Palettes menu or Check Duplicates in the Options menu.
The menu positions you saw in earlier AC versions were overridden in the WE settings manually to place those add-ons into more logical places — taking precedence over the default positions defined by the add-ons' code.
So, the interesting question is: why don't the add-ons appear after installation? If those commands are not part of the WE, they should appear automatically... unless there's another bug somewhere 😞
