Yes it was pretty obvious where all the DLC was going to take place in the vanilla game. Gladio's was painfully obvious but most fans guessed pretty easily where Prompto and Ignis' were going to take place. It really just was as simple as looking at points in the game the character wasn't in the party. Gladio's DLC is pretty easy to skip, but both Ignis and Prompto's DLC fills some major plot holes concerning the empire that made the later chapters jarring in the vanilla version of the game without it.

I don't really mind the Royal Edition fixing the story issues, I mean it's better than having it left in an Ultimania or even worse, a developer interview where they talked about all the stuff they wanted to put in. I kind of think of it like SMT3: Nocturne, because the Maniax version we got in the West was the director's cut that actually added a bunch of stuff to help the story make more sense for players. P3: FES does the same thing. So I see Royal as more of a director's cut. Would it have been great to have it like that when it first came out? Yes, but fans were seriously pressuring SE to release the game and they made a bad call on giving into the demand. The service model idea was just a bad idea overall, and so far, SE has taken that to heart if VIIR is any indication. Still, I feel the fan expectation for XV was so high that even if most of the DLC/Royal edition content had made into the original release, the game was still likely to be lambasted by the fanbase. It was a lose-lose situation for them.