nwn_deadman: A logical argument for you (I posted a variant a couple of pages ago, but you did not deign to answer.)
A Miracle is a prerequisite for the creation of a Tome of X, which grants an inherent ability score bonus. At no point does it actually state that miracle is cast during its creation- therefore, it is implicit that a cleric whom can request miracles of his deity has reached a power level such that his deity will aid him in the creation of a magical item. In return, the caster must pay 5000XP per inherent bonus increase.
At no point in the DMG does it states that having the appropriate prerequisite spell means that the spell is cast during the creation- ergo, Miracle is not necessarily cast during the manufacture of the book in question- but that the fact that the cleric has access to Miracle means that he has the capability to craft the book. The ability to cast Miracle is required, but this may be merely to request his god to help craft the book- it does not infer that either a) Miracle is cast and hence b) Miracle can grant inherent bonuses. Just because the Miracle enables you to craft an item which grants the corresponding power, it does not necessarily mean that it can simulate the power of the item crafted. A wish could, conceivably, generate a +2 Headband of Intellect. It cannot generate a +2 enhancement bonus on an individual ad infinitum.
The second counter-argument is that the spell prerequisite does not duplicate the item when the spell is cast normally. There are a myriad of strong examples listed already, so I won't bother to reiterate them. The case of fireball not being able to replicate a flaming weapon when cast in a combat, but being a prerequisite for a flaming weapon creation is one such example.
I hope this is a logical argument that would sate your standards.
Alternately,
OF COURSE IT DOESN'T WORK? Are YOU STUPID?!!!
IT's LIKE TALKING TO CHILDREN HERE!!!
Sometimes, you GUYS ARE FEEBLEMINDED!!! and you can't even spell DEITY SOME OF THE TIME!!! (page 4, nwn_deadman)
Incidentally, PHRENOLOGY! AUTOHAGIOGRAPHICAL! BROBDIGNAGIAN! PREANTEPENULTIMATE! ESTERIFICATION! I have a LONG vocablurary, therefore MUST BE CLEVER. THEREFORE, must be RIGHT!!! You guys are STUPID!
may be more your style...