I can't comment on the larger theory since I haven't played FFV, but regarding this bit...

Quote Originally Posted by mallleable View Post
what's in the other tower, considering Flare is just a level 50 BLM spell, Ultima?
If Flare is just a level 50 BLM spell, then Holy is just a level 45 WHM spell. So if you're speculating that there's some special sort of Holy spell then there can equally be a special sort of Flare spell.