The game does a pretty good job of that though, there aren't many instances where this is relevant, and when it is the general rule of thumb is that the entirety of ARR comes before the entirety of HW (and then SB and so on). Some times that should be noted are the ARR CUL questline taking place before 2.5, the ARR DRG questline taking place before2.42.55, Tam-Tara HM taking place before PotD, binding coil taking place before 3.4, and crystal tower taking place before 3.5 (while these last two take place before 3.0 anyway, they are directly referred to as past events in those patches).
Given the route the story is taking however, I expect to see a lot of shifting about (both geographically and character development) for side characters who may appear in side quests, so expect to see more of this (and remember that everything in SB comes after HW).