Everyone seems to forget that Blade Runner was visually amazing, aurally engrossing, beautifully and atmospherically shot, a cinematic masterpiece... that utterly flopped at the box office. It only started getting its "cult status" after several years in second-run theaters and home-video release. So I don't know why the studio expected anything less with BR2049. It has a niche audience of hardcore fans who are not and never have been the general moviegoing public. It would only ever have niche appeal. It had to be gone into consciously as a labor of love you expected to lose money on -- at least initially.
Same with Dune. The story requires you to think, and a lot of moviegoers go to movies to get away from having to do that. The Lynch version might have been fantastic and definitive if not for studio interference and a couple questionable creative decisions (eliminating the stillsuit hoods and masks -- and capes -- in order to see the actors' faces, ornithopters that didn't flap their wings, and the ending that gave immediate payoff rather than leaving things open). The casting was great, the production design was extraordinary, the score was -- and still is -- wonderful and fitting. And if everything that was shot was used and all the VFX work had been finished, a three-and-a-half-hour-with-intermission Lynchian Dune would not nearly have been as inaccessible as the theatrical cut ended up being.
So yeah, it's vitally important that the studio knows this will only ever have niche appeal, and that Denis can make it as long as he needs it to be to tell the whole story. At least with Lynch's version, Frank was there the whole time to give the nod or veto to all the choices, because Lynch wanted to make sure it was true to the author's vision. And at least Denis had Ridley involved on BR2049 to make sure this new delve into that world lined up with its creator's sense of it. With this Dune, though, Denis is having to go with his best guess, and probably relying on Brian Herbert's sense of what his dad would have been okay with.