I hope this hasn't taken things too far away from the original question: How do you account for monstrous extras who are too low a CR to show up on the Exp charts, but which still contribute to the scene.
Well, I think I answered that, but I still insist the problem is that 3.5 has no concept of balance whatsoever. Not only is chargen/advancement utterly broken because charop/system mastery plays an excessive role in character prowess and intuitive builds are under powered, but 3.5 rebalanced the game based on the assumption that parties would use charop and rejiggered monsters to higher CR and with higher CR accordingly. This only exaggerated some of the problems in 3.0 such as the fact that they had deliberately decreased dragon CR by 2 under what playtesting had suggested because "they wanted dragons to be scary" (which is as nonsensical of a design decision as I've ever seen), and the CR's are often wildly inaccurate (consider them guesses by up to +/-2). Then there are individually hugely poorly thought out save or suck abilities such as entanglement, web, and as you note the 3.5 version of Blasphemy. The 3.5 version of Blasphemy is involved in a charop build that by 20th level can defeat most gods by raising caster level up to about 100 through a variety of poorly thought out rules, and then simply outright killing pretty much anything.
As a mini rant, 3.5 made a big deal of 'fixing' Harm and Haste, two spells that were arguably broken in 3.0. But then it went and broke with poorly thought out unplaytested changes scores of spells that weren't broken in 3.0 including Blasphemy, which used to be statically capped by the HD of the target and not relative to the caster level of the caster. The result was an 'Ok' crowd control spell became utterly game breaking. When I saw the 3.5 Player's Handbook, which I'd expected to be basically 3.0 with the errata in it, I never bought a book from WotC again. That was the breaking straw for me when I realized that I could write better rules than WotC, so why in the heck would I pay them for this crap.
There are some problems here that can't be helped owing to the games design. CR has to assume a balanced party with the range of options it expects, and sometimes that doesn't happen. But it doesn't help that WotC never seems to think through the consequences of their mechanics and address, "What happens if..." Likewise, LA, ECL, and a good portion of the templates are just busted. If you are trying to be a RBDM, there are tons of things you can do that in theory produce a creature of CR X, but which in fact hide the real increase in difficulty. For example, size change isn't normally a major increase in CR (if at all) because size increases carry so many penalties, but if the monster relies heavily a on grappling attack can get a huge boost in difficulty. (Likewise, a monster that can't be grappled and doesn't depends on physical weapons gets a huge bonus in capability but no increase of CR if you decrease its size.) There are also synergies which the game doesn't take into account, such as anything that gives a regenerating monster immunity to the sort of damage that bypasses regeneration, such as a troll with fire resistance.
In short, if you don't rewrite the whole darn game, then I think you have to recognize CR is just a ballpark number and not a firm contract. Who can't go, "Well, I'm just following the rules.", because it's just as possible to optimize monsters for a given theoretical CR as it is PC's. The DM can make pun-pun's as well.