i90 AF and the 'Primal' weapons.

[Norondor]

I'm not sure about the mechanics behind conjury and thaumaturgy or how the weapon mechanics work in order to augment the magicks.
But the following strikes me as strange:
* The Crystal Tower is the tomb of the first Allagan emperor
* Allag was founded in the Third Umbral Era.
* Allag flourished during the Third Astral Era.
* Allag fell as the Fourth Umbral Era started.
* The discovery of magick brings the Fifth Astral Era.

Why does the crystal tower contain weapons that augments magick?

Allag certainly knew of magick, and their civilization was apparently the dominant cultural influence in the world at the time of the third astral era -- their fall would have probably been a new dark age, and the fifth astral era probably marked an independent re-discovery of magick. At least that's how i'd interpret it!

Did any other civilisation after the fall of Allag guard the tower (and left weapons behind) for some reason?

If i'm not mistaken, don't the gigas claim rightful dominion over the ruins at st. coinach's find? I think Acheron looks a bit giant-ish...

No idea! They had a thousand years; Earth's came pretty far in the last thousand years. Then again, Ishgard had about 1500 and they didn't get all that far, did they.

Hey, the western world hasn't yet had to tussle with an infinite army of mind controlling dragon mutants, so credit where credit is due! (and it is all due mighty halone, may she see our enemies driven before us)