It seems after Yoshi took over the plot was adjusted to what we've experienced.
I'm sure the first cutscene wasn't refereing to Dalamud, yet it was shifted and positioned in such way that it seemed so.

I'm sure they did the same for the song answers, and I've taken a shot to find meaning in the lyrics.
If you disagree in parts of them, or find a different meaning, or find meaning in those parts I couldn't understand, please post them and I'll update it.

I close my eyes, tell us why must we suffer
Release your hands for your will runs asunder
My legs long tired, tell us where must we wander
How can we carry on with redemption beyond us

To all of my children in whom life flows abundant
To those alive
To all of my children to whom death hath passed his judgment
You are destined to die
The soul yearns for honor and the flesh the hereafter
Your spirit will want to fight, and you'll tire yourself so that your body will want to die
Look to those who've walked before to lead those who walk after
This happened before, take lead from the Archons

Shining is the land's light of justice
Ever flows the land's well of purpose
Walk free, walk free, walk free, believe,
The land's alive, so believe
???. Maybe embelishment. Maybe it refers to the aether flowing through Eorzea or to believing on the twelve?

Suffer [feel] (me) lonely [face] (me) weakness [teach] (me) evil [fear] (me)
Suffer lonely, learn from your weakness (meaning team up), evil will fear you
Although [feel] (me) one must [face] (me) stumble [teach] (me) listen [speak] (me)
There will be set backs. Listen, learn.
(Although we) [speak] we (might) [tell] them (we must) [tell] them (land of) [hope] hope
Have hope
(Mother) [hope] hope (father) [wish] wish (every) [wish] wish (has a) [roam] home
???
(We must go) [roam] go (listen) [roam] go (suffer) [roam] home (sanctum) [swim] leap
Travel through the world. Have experiences.
(And as) [speak] we (wander) [sleep] sleep (answer) [sleep on] sleep on (on)
???

Now open your eyes while our plight is repeated
Armaggedon is coming again
Still deaf to our cries lost in hope we lie defeated
Your prayers will be ignored and you will lay defeated
Our souls have been torn and our bodies forsaken
Refers to separation of spirit and body? Or maybe just means you've been defeated.
Bearing sins of the past for our future is taken
Your future is doomed because of the sins of your ancestors

War, born of strife these trials dissuade us not
Garlean vs Alliance war
Words without sound these lies betray our thoughts
???
Mired by your plague of doubt, the land she mourns
???
Judgment binds all we hold to a memory of scorn
All you know comes to judgement held with hate (bahamut taking revenge?)
Tell us why, given life, we are meant to die? Help us in our cries!

Witness (we) suffer (we) borrow (we) reason
(We) follow (we) struggle (we) wander (we) listen
(We) whisper (we) shoulder (we) addle (we) weather
(Please) answer (you) answer (me) answer together

Thy life is a riddle to bear rapture and sorrow
You are to be seized by violence
To listen, to suffer, to entrust unto tomorrow
To learn from this and suffer it, and believe in those from tomorrow
In one fleeting moment from the land doth life flow
Everything will die, instantly
Yet in one fleeting moment for anew it doth grow
But we will prevail, and rebuild in no time
In the same fleeting moment thou must live, die and know
Your life will take place in this lapse of time