Anubis-
I think that your argument is fundamentally flawed because the only pertinent argument I have witnessed (though I have not been following the entire saga) is that be rejigging ability scores to either overpower or underpower the said creature, U_K's system can be broken.
Well, quelle surprise!
Any system can be broken if the
reductio ad absurdum approach is taken. The magic item creation system can be very heavily abused if this approach is taken, as can any 'point-based' system. Indeed, it is possible to argue (taking your line) that the point-buy ability generation system should not count ability scores. For example, a Fighter who takes Charisma 18, Intelligence 18 and the rest at 8 is clearly inferior to one who buys 16 Strength, 16 Constitution, 12 Dexterity and 10s in the mental abilities. Yet there is no complaint that the former should reflect a 'lower point' character simply because those ability points (or 'CR points') are spent injudiciously.
Indeed, your line of attack could be used on other aspects of what is (by and large- I have not come to this without raising a few concerns of my own!) a decent CR estimation system. For example, I could power-build an extremely powerful 10th level wizard, just as I could build an extremely weak 11th level wizard (by, for example, having a mere 9 Int

). Your logic would state, therefore, since a counter-example had been found to the maxim that 'in general, higher level=more powerful' than using levels as a component of CR is a nonsense. Do you see? Nearly any component of CR laid out by U_K in which there is some degree of discretion can be made to look foolish- but only by taking extreme examples, such as the Persona Diminutive.
Moreover, your core argument is very difficult to substantiate. Given that (hopefully) most DMs have some degree of judgment, a character such as the Personal Diminutive is unlikely to be built. Rather, if a DM wishes to generate a custom monster, it is clear that a monster with higher ability scores is more powerful than a monster with lower ones. The irrefutable case is one where every one of the monster's ability scores is higher than its opposite. Surely, then, the monster's CR should reflect this increased power.
Essentially, Anubis, your fault is taking an extreme example and then back-extrapolating to say that the system is faulty. Yet anyone can do this to any system. Any system will break down at some extreme. Some counter-example can be found if we delve far enough into the realms of absurdity. The Persona Diminutive does indeed break U_K's CR system. Yet that does not invalidate it for the mainstream.