I think the dungeon was designed and QA'd with the old MP costs and AoE cure in mind. That's really the only way they could justify the heavy toll of melee sponging AoE damage for large portions of the fight. With speed/efficiency in mind, there's no way they could intend for a number of melee DD to sit out parts of the fight for fear of taking AoE/ghost damage, or expect melee to avoid taking the damage in the first place.

As for the part about Matsui being worried about releasing content before Jobs, I think its actually the opposite of what you were thinking about making the encounter harder by taking away Armoury flexibility. I think he knew that the dungeon would be very difficult for players who did not have multiple classes leveled or were limited in main class role flexibility. Perhaps Jobs would've made certain parts of the dungeon easier by basically negating or trivializing the more difficult portions of the dungeon.

For example:
  • Batraal Laser Show spam ----> PLD pops Invincible (magic invul. too) for 30s
  • Melee all at 20% Health on Batraal or Ogre and no MP ----> WHM pops Benediction
  • Last 20% on Batraal or Wave of Skeletons ----> BLM pops Manafont and nukes for duration.
  • Last wave of Skeletons or Batraal last 50% (depending on how u handle them) -----> MNK pops Hundred Fists, Each RNG hits Eagle Eye Shot, WAR goes Mighty Strikes and everything dies in seconds (a few seconds faster than current AoE/mana burn strat I guess).
We haven't had much to do in the last 11 months other than level, so the gamble paid off I guess, as the main complaints about the dungeon's diffuculty now are from people who do not have multiple classes leveled for whatever reason(s).