It was kind of a joke, but also kind of this:
I think when you're handling a massive 150M+ production (nearly twice that with prints and advertising included), you have a higher responsibility than just making "good art." It's not just a movie, it's this massive investment. I'm one of those that enjoyed 2049 but still thought it felt slow as molasses at times, so I believe a little trimming here and there could've helped making it more palatable to the average moviegoer without compromising itself. It's not like the length is the problem, it's barely 15 minutes longer than some comic book movies these days. And yet most complaints of people that disliked it "oh it's sooo loooong, sooo boooring", it's almost becoming meme-like. That's about pacing and editing and rests solely on Villeneuve and his editor.
Sure, Villeneuve didn't go overbudget, and he was handed this project, in a way. But when you reach budgets of a certain level you probably do need a little compromise to make the money back. Good for him I guess. Not good at all for Alcon.
Alcon is for sure insane. Denis Villeneuve didn't even have final cut in the movie. They just let this happen.