Yeah, 12 levels in a single class doesn't a cost anything at all but 12 levels in another class perhaps.
I just think it's an utterly silly argument.
And technically, by your decision, being able to find 6 books of +5 inherent bonuses is up to DM interpretation, so that might not have been able to happen either. The abilities of the wish spell which are the actually effects of the spell are clearly laid out in the description of the spell, and not up to DM interpretation unless Fireball or any other spell is.
Also, being able to have cast Permanency to make a spell permanent only takes time when you have a Rod of Excellent Magic, it doesn't cost anything else.