I really liked your example, but have a couple of comments. Making its attack bonus suddenly +11 is, in my opinion, disconcerting, although it depends how you're doing it. Don't forget that many other checks might come up involving its base attack bonus and/or its strength, so you really ought to adjust one of those components. For your example I might have just reduced its HD a little so that it isn't so good at attacking, and if it doesn't have enough HP, give it some more Con.
Your solution changes a few more things, though. It's unfortunately not that simple.
Lowering his HD lowers his BAB, but also his saves. Raising his Con score to compensate then increases his Fort save, but his Ref and Will saves will be hosed and now (in this example at least) his Con is unreasonably high; I was already pushing the envelope with a 22. His skills and feats are also lower, so if I had chosen a feat loadout that I liked a lot (and a lot of feats have feat prereqs, exacerbating this problem) I'd be forced to abandon it.
It's not always going to be a big deal, but it does two things that I think are bad. First of all it simply adds time and headaches to the process of monster building.
Second, it restricts what the GM can accomplish unnecessarily. In my opinion it's not even good simulation. Why is it impossible for a monster to advance by getting tougher and tougher without also getting better and better at attacking? A giant tortoise doesn't seem to get any more lethal as it grows, but it definitely gets bigger and more resilient.
3.x monster creation is a set of guidelines. They are useful. I got a lot of good games out of them. But they shouldn't be a straight jacket, and when the monster guidelines yield a result that doesn't make sense in the gameworld, doesn't match your idea for the monster, and doesn't match the CR guidelines that you are trying to get to, I see nothing wrong with editing the numbers directly to ensure a more useful outcome.
As [MENTION=5889]Stalker0[/MENTION] noted, you can always give the dolgrue
Maddened with Pain (Ex): Dolgrue live in constant agony as a side-effect of their creation process. As a result, their BAB is considered 4 lower than it should be for their HD due to the constant distraction.
EDIT: If you get your fun out of running a simulationist game, where both player and GM have to play by the rules and the enjoyment is derived from seeing how the intricacies of the rule system crash together with player choices to produce an emergent gaming experience, that is awesome! In that case my post, and my whole argument in this thread, won't apply much to you.
By the same token, that sort of game values a monster creation system that is not entirely suitable for my gaming style. I want to be able to tailor monsters and encounters to challenge my PCs. I want them to be stymied in some encounters until they figure out the "trick" of it, or maneuver the enemy into hostile terrain, or whatever. That requires pretty fine control over the monster's stats, and I don't want to have to wrestle with the system to get that control.
To each their own, of course. I don't envy the designers this task, but the ideal would obviously be creation rules than allow either of these philosophies to be applied.
Maybe I'm a bit grognardy, but for me, "historically" and "traditionally" means "1e/BX/BECMI" era D&D and earlier.
- I guess I found it difficult to express my ideas in number form without very explicit mechanics 
