Just pick up and do quests/run dungeons as soon as they become available. This will, with very few exceptions, get things done in the "supposed" order. (Only exception I can think of is PotD which becomes available quite early.)
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There's some minor differences in scenes from 2.55 (Before the Fall - Part II). Depending on whether you've started the DRG questline or completed it, you'll get alternate dialogue when Estinien walks into the intercessory during "The Wyrm's Roar." If you haven't started it he treats you as a stranger; if you've started but not completed it he acknowledges you; and if you've completed it, he will acknowledge you as a fellow Azure Dragoon.
It might be 2.5 instead of 2.4, but the first time you meet Estinian in the MSQ is definately before steps of faith. He is introduced by Aymeric at a meeting, and if you have beaten the DRG questline, he will acknowledge you as a fellow azure dragoon.
Edit: Nvm, Cilia explained it far better than me
It's actually both. In 2.55, Estinien will acknowledge you based on your DRG quest completion, implying that the DRG job quests can be considered canon anywhere in the 2.0-2.55 bubble. In Heavensward proper, Estinien will acknowledge you as another Azure Dragoon regardless of even job crystal possession. A WHM-main friend of mine who started with Heavensward was very confused by this.
I think the simplest metric we have is whether or not the reference to X content appears in voiced dialogue or not. Since voiced scenes don't use text-replacement macros like regular dialogue, they have to make the choice to either solidify continuity or evade direct references entirely.