That assumption is wrong. While Germany starts the scenario controlling those territories, they are still original Russian territories, similar to how the Chinese territories controlled by Japan at the start of the games are still original Chinese territories, preventing Japan from building major ICs on anything but Korea.
Then why in the set up instructions does it say put a German control marker on the territory, as well as units? Just a unit on it should be enough. Every time you take an enemy territory do you put a control marker on it? I don’t.
You can play however you want of course. But the rulebook clearly states:
If you have captured the territory, place your control
marker on the territory and adjust the national production
While the emblem printed on the map indicates the original controller of the territory
the control marker indicates the the actual controller of the territory - as ColoneCarter pointed out.
There are some rules where the distinction between original and actual controller is of importance.
The 3 IPC bonus for Russia is only one example. The territories you mentioned can never become
“original German, Italian, or pro-Axis neutral territory that the Soviet Union controls”.
When the scenario begins Germany has already captured some original Russian territories.
If Russia takes them back, they will be original Russian territories under Russian control.
So better avoid confusion.