Chekov's only turn in the seat was during THE FINAL FRONTIER, correct? So then either Scotty elected not to assume command or Chekov has exceedingly good connections now. Obviously both are lieutenant commanders at that point. Would've been nice to see Scotty take command in the film sequels on occasion, anyhow.
I would say in TFF, there was too much concern about the ship functioning properly for Scotty to take his eyes off the engineering ball, so to speak. So he probably respectfully requested command fall to Chekov in that case.