I really believe that Kondou understood the confession but there are other problems that comes with that. He's an old man that has zero to none confidence since his previous relationship failed, on top of that Akira is just a young girl that can be his daughter.
Those 2 things are probably messing with his head and that should explain his reaction after the confession. On a side note, the animation is incredibly good and the studio is being faithful to the source including details that really shows the feelings of Akira.
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