They absolutely are elemental-based - it's spelled out clearly in the lore, in multiple ways.
Each constellation is the gate to an elemental heaven.
The legend of each constellation references the two gods associated with that element (as noted in the character creation where you choose your guardian deity).
The cards themselves are represented not only by 'colours' but their elemental symbols: a tree (earth), sun (fire), lightning-bolt, gust of wind, water-jar, snowflake.
There are unique visual elemental effects as you play each card.
And it's directly written in a table of information about the arcana in the lorebook.
The original card effects also seem directly inspired by the elements, and the constellations probably invented to fit them:
Earth = defence
Fire = attack
Lightning = recharge
Wind = speed
Water = refill/refresh
Ice = ??? (sharp spikes = crit?)
Certainly that's how I learned to associate the cards with their effects.
Would you like to point out where those issues actually are? Have you actually gone back and reviewed the story, or are you just going from memory?
Nobody answered me the other day in the discussion about AST lore when I asked for specific examples... it fell utterly silent as soon as I posted the actual descriptions for all the cards - as they were both before and after 5.0. Four are unchanged, the Bole minimally, and only the Ewer altered to reflect its new effect on physical ranged fighters.
I've played the story twice, three times for 30-50, and read through it a lot more than that. Besides the initial battle-tutorial text (which has been removed), I can't think of a single instance where we were asked to use a specific card. It's all "cast Aspected Benefic on the injured civilian".
Again, Garland Tools has the entire script. If you think there's a problem, find the quotes and show where the altered lore clashes with them - if they haven't already fixed it.
And I still have the saved text from 4.4 if you're certain there was something that used to be there, and isn't now.