I posit that the Cooper we saw was actually a combination of all 3 "coopers".

He had the coldness of Evil Dale Cooper (from his shooting the 3 cowpokes, to his general attitude).

He had the lostness of Dougie (notice that his eyes slow blink when he is driving, and a few times he kindav doesn't seem too aware of his surroundings).

He has the methodical thinking of Cooper Prime (he displays intelligence, and in general is taking everything in).

What he lacks is the complete "good nature" of Cooper Prime.

There is most certainly something 'off' about his behavior and I really think it's because all 3 personas have been combined into one.