You don't understand "doing well" is not about movie which makes the more money. Comparing it moonlight is stupid.
It's about being successful, Moonlight was a very successful movie, and success for a movie is measured basely on two things, one is the narrative surrounding the movie (critical reception, public reception etc) the other one is if the studio actually won or lose money with the movie.
Blade Runner was liked by critics and the public that saw it, but it was branded a failure because they lost money.
In the history of Best Picture Oscar's, you almost never have movies that generated losses for the studio, one of the main reason is that like someone else said here, the studios never push a unsuccessful movie, Oscar push cost money, and if you add to that that Blade Runner is a Science Fiction, a genre that never had much success with the Oscars, especially in the last 20 years, it's pretty obvious that Sony would never made the oscar push it deserved.
Another thing to take into account when reading Villeneuve's response, is that it is a response, someone asked him a question. He didn't make a twitter rant after hearing about it.
Also, he actually never talks about himself, so it's not about him wanting an oscar.