Would Russian nobles constrain a German Kaiser ruling Russia?

Would the German-Russian union depend on the Kaiser's ability to displace the entrenched Russian nobility?

Only partly: access to German officers would reduce his dependence on Russian nobles for army and naval leadership.

Wilhelm would not rely solely on Russian nobles for military leadership. As ruler of Germany, he could draw on German officers for the army, navy and wider armed forces. That alternative would reduce his dependence on entrenched Russian elites without making their position irrelevant.