It's probably more a marketing thing. I'd guess the skimpy outfits appeal more to the Japanese audience, and the Nintendo outfits will fit better in other territories.
That's true as well. In the West these last several years there's been a major push to improve depictions of women in gaming. A lot of these demands are usually how they're shown in the AAA blockbuster titles which are mostly M rated in the West as well.
Yes, Fatal Frame is an M rated title but considering the push for more positive portrayals of female characters in Western markets includes Mature games as well, it's not hard to see why Nintendo thought replacing what was basically sleazy looking porn outfits into more friendly looking Nintendo cosplay customs would go over better in the West. So even though Fatal Frame is very niche, in Nintendo's mind changing the outfits might make the game more appeal to women in the West now.
This is likely true, although when some regions get the costumes and others don't it feels like over-protective pandering instead of a stance that the (overall) company actually cares about.
Of course, that's how localization works. The choices NoA or NoE make won't be the same as the ones made in Japan.
I will give credit to the localization team for fighting to improve how women are viewed/treated in games. While I think the removal was probably unnecessary, and that the replacement costumes are an absurdly bad fit for the game, the intent is clearly good. Despite my complaints, I can get on board with that.