Just because a team is smaller and more agile doesn't mean that they are any less inferior or superior to a studio like Naughty Dog. You also have to realize, technology changes overtime and so development evolves as well. You can still focus on innovation and make a big/ambitious title. Its not a indie studio if that's what you're implying by any means lol.
Also, not to get into a pissing contest but Naughty Dog is not really know for its "groundbreaking innovative gameplay" let's be real. They're more of story tellers rather than gameplay. Uncharted and TLOU never had anything ground-breaking in their gameplay mechanics, it was the theme and how the story is being told what made these game so highly praised and sell. The mechanics in these games worked well for the theme and were well executed but they were never ground breaking. Naughty Dog also refuses to make open world games which in my opinion is a shame, but maybe they know that that's just not their strong suit and that' fine.
So I am not sure what you mean "Naughty Dog" levels. Naughty Dog was never ever a king of gameplay. If what the article states in regards to innovation and not scale is true then that would imply that The Initiative is looking into creating a more consistent experience rather than throwing the player into a giant massive open world which is actually what Naughty Dog does these days. Dark Tide still could be an open world game but it doesn't mean it needs to be absolutely huge, because more empty spaces doesn't usually mean higher quality in the first place. If anything the whole "innovation" thing and smaller "Scale" actually fits Naughty Dog description pretty well, Naughty Dog tries to innovate already good mechanics, into more better mechanics and evolve what's already there, but they never tried to or even attempted to reinvent the wheel and that's fine because it works for them. Last of Us itself or Uncharted are not very big games in terms of scale, they never were. UC 4 and TLOU 2 are more open ended sure, but that's it.
Horizon Zero Dawn also was an open world game, but it never focused on the scale either, at least in my opinion. It took a lot of the mechanics that already existed in other games like Far Cry where you collect mats and craft using a navigational wheel hud, the crafting is 1 to 1 with Far Cry lol. The only innovative part was fighting the mechanical dinos, and even then that was obviously inspired by Monster Hunter with Horizon's own twist with breaking the mechanical parts. I do not consider Horizon Zero Dawn a massive game in scale, the world is quite small compared to something like Zelda BoTW or any of the AC/Far Cry games. But its more consistent with content and activities rather than fluff. The Initiative could be taking a very similar approach.