After thinking over any way to reconcile this massive contradiction I am only capable of concluding that Masuda & Ohmori either exaggerated or flat-out lied about this particular development detail in a misguided attempt to make Game Freak look better. No, this explanation doesn't sit right with me either, it seems just as weird and out of character as you think, but I only default to it because all the alternatives seem even more outlandish
I'd like to propose a different vein of thought: that while Masuda & Ohmori's statement is untrue, it wasn't necessarily their fault that it was so.
Ultimately, this interview (and others) is marketing propaganda - TPC publishes such articles to promote their rose-tinted narrative of the franchise. For example, this article states things like "We always take player feedback into consideration" or "We always want to come up with new surprises for our players with each new Pokémon game. This is our first time introducing free camera movement in the series, so we're excited to see how our players will respond to it once they get their hands on the games". The first statement is flatly untrue, and the second is incredibly dumb beacuse every RPG that's
not trying to emulate a retro style already has free-cam - there's nothing to learn from adding it.
Game development is, obviously, nothing like what they state. It's difficult, with lots of aggravation and conflict due to the nature of a collaborative project. Rarely do large studios
not have issues with crunch culture and systemic abuse. GF's horrifically brutal 3 year dev cycle is a clear testament to this. It's sad, but it's reality. But, this is a reality that the TPC doesn't want publicized (obviously).
So what does that all mean? It could mean one of three things:
1) Masuda & Ohmori deliberately modified their statements in the interview beacuse they were conscious of the need to promote GF's image (as you've stated).
2) Masuda & Ohmori gave an interview, but TPC modified the interview statements to better fit their goals for Pokemon's public image.
3) Masuda & Ohmori never even given an interview, and the entire article was crafted by TPC for the purposes of advertisement.
Personally, I would assume it's one of the latter two. In interviews with outside individuals/media, the interviews are similarly rose-tinted, but they tend to always skirt around game development questions. Even when they get pressed on such questions such as Dexit, they'll only make vague statements. It's easier to spin the positives of features than it is to actively spin details on game development. Hence, they avoid it. But, in a vacuum where they can rewrite the narrative at their own leisure, they might be more willing to do so.
Ultimately, it's unlikely that we'll ever know what actually transpired. But, it's important to understand the context of this and future interviews. It's an advertisement, and should be thusly interpreted as such.