Jan,
Maybe this step is necessary because of concurrent licenses.
Let's say you have 10 users that have 10 concurrent ArcGIS Desktop licenses, but your company only has the budget for 2 concurrent 3D Analyst licenses. Once 2 of those 10 people have activated the 3D Analyst licenses, the other 8 won't be able to use this extension. Once those 2 are done with the extension, they will deactivate it and the 2 licenses will return to the pool, where other people can activate it from.
If you have only one single use license for ArcGIS Desktop and one single use license for 3D Analyst, then yes it would make sense to not having to activate the 3D Analyst license.
Hope this helps!
Tim