Amazon owns around a dozen skyscrapers in downtown Seattle. Amazon has a massive number of employees in downtown Seattle, and whether those people are downtown or not makes a significant difference to the real estate values in downtown Seattle. Making their employees come into the office may in fact mean a significant financial reward to Amazon, but not because the employees are doing better work.
Also, Andrew Jassy specifically has a number of personal financial interests in the Seattle area, including the local hockey team and the nearby Key Arena. Keeping downtown expensive and full of people is in his personal interests.