It could have been improvised! Maybe there was more planned for Lavasteam—it would make sense if there was—so for whatever reason they had to cut that extra content out would mean that the story was improvised or modified to some extent. As for the other points, I'm not really sure. I did find it weird that Sock pointed out Mari to Jowee; I guess that was just to gain more trust from Jowee and the player since he knew they wouldn't be able to reach her in time or something?
I kinda feel like the ending was at least half improvised. While there was some foreshadowing in the first game (Heather's face, and Mike saying it must be a dream), there are too many inconsistencies for me to think was completely planned out. Who knows? Maybe Heather was originally going to be the one in a coma.
Speaking of Mike, there is this one scene in Lavasteam that has NOTHING to do with the final story. After the Robosa go crazy, Mike leaves Turtle Rock, and enters the second section of Lavasteam. He is then chased back onto Turtle Rock by the Robosa. Mike also exclaims at one point that this always happens to him... So what was that? Were the Robosa once planned to invade Turtle Rock? That scene always confused me.