There are arguments for and against using these rules in organized play and I wanted to explore them a bit and share my opinion and why I have that opinion.
Beyond the obvious legality, these rules allow for a truly staggering degree of variety. They also allow players to build whatever army they want for crazy levels of customization.
The modeling opportunities are also huge. We've all seen some of the amazing conversions that people come up with such as Ork or Chaos Imperial Knights, looted vehicles, Chaos IG, etc. Cool! I love that stuff as do most of you do, I am sure. The creativity inherent in our hobby is easily one of the best aspects of it.
With no limitations, which is what 7th ed indicates we can do if we choose, you will see a larger percentage of players making the choice to take these cheap, accessible units in armies that normally wouldn't or couldn't. Tyranids with Coteaz or a Culexus or a Knight? Draigo with Daemons? You will get a large number of players that choose to include these powerful units for no other reason than to buff their army.
The downside there, is that you will end up with hodgepodge armies that don't have a unifying aesthetic or show a lovingly created army with a clear theme. And, you see the same units in more and more armies simply because, why wouldn't you take them? It creates less diversity in the game and more unfun combos.
Time to get off the fence...
In the meantime, with Come the Apocalypse Allies allowed, for every 1 army that is truly an awesome work of art, you will get a lot more players that simply stuff a good model into their army because they can to gain a power boost. You then throw the fluff out the window in the process. That to me, is not a profitable exchange.
While I don't think that we should doggedly adhere to fluff in all decisions we make, completely forgoing it is giving up a lot of what makes the 40K universe so cool. I honestly do not want to play against a Deamon Army with Grey Knight allies. I don't want to see an Imperial Knight teamed up with Nids. Even if you do cook up a cool story about how it happened to come about, my personal preference is to see the fluff have some impact.
Enough to keep the factions cool and relatively unique. Therefore, I prefer to play without Come the Apocalypse allies or with Unbound lists in organized play. I think the game is more enjoyable for more people with some restrictions such as those listed above.