UK, I don't know if you created that document, but it's VERY hard to read. The fonts do not serve the document well.
That said, I think that PDF fails to understand the main prupose of CRs...to SIMPLIFY creating challenges for the DM. If I'm sitting around, calculating long formulas using percentages based on hit dice, ability increases and so forth, that's time I'm not actually spending playing the game.
Second, CRs are a guideline. Abilities of individual parties vary wildly, so that's where ELs come in. The system in the PDF seems to emphasize radically increasing most CRs, and then using ELs to lower situations back down....all of which doesn't seem to provide much more utility for the DM; it's just reinventing the wheel to satisfy the author's sense of verisimilitude. There's nothing wrong with that, but it doesn't sound like it helps the DM much more than just simply 'eyeballing' it. A group with a Radiant Servant of Pelor is certainly more likely to deal with a high-powered undead or creatures who use darkness than one without. A group of four barbarians is going to find a spectre much more challenging than a group of four clerics. The CR system needs to deal with that.
At low levels, the CR system has much less of a problem with this. But at higher levels, with insta-kill 'save or die' powers, calculating CR becomes more problematic. Especially when you consider that the characters LIVES are considered a resource. If three of the players survive with all but one spell intact, they've maintained their resources in line with the formula. It's terribly unsatisfying, but there it is.
Note how monsters are filled with abilities that would be incredibly powerful in a PCs hands...but the monster is only going to get one combat to use them, generally. My players party level is a collective 19...but they've defeated a CR23 creature, with no loss of life. They followed that up with defeating a Paragon half-fire Elemental Beholder. Under the CR system listed above, I'm assuming both of these encounters would have been in the 40s or higher. Which illustrates that the CR system is a tricky beast, in either system.