Glyfair said:
Because it's more fun that way.
This depends entirely on what you are trying to get out of the game. If your goal is a fun shared experience, then it may well be more fun that way. If your goal is something else, you may not care for novels to be canon for the setting.
One reason to ignore the novels is if you do not like how the writer presented a certain topic. Another reason is if the novel contradicts your game.
For you, it may very well be that using the novels as canon adds to the experience, but that isn't the case with everyone.
The shared experience and being able to compare their experiences was a big draw. I think it would be a big draw today, if it wasn't diluted by so many options. I think taking that experience away isn't a good idea without a good reason.
I think forcing the shared experience isn't a good idea without good reason. The groups that I've run games for do not hang out with gamers and would not gain anything from this shared experience, anyway. Others that I run for would gain something.
The most important thing to consider, however, is not the shared experience. It's the campaign/game. If sticking to the novels as canon detracts from the game, then it shouldn't be done. Furthermore, your shared experience assumes that the GM actually reads the novels. If I am running an Eberron campaign, I am under no obligation to purchase and read the novels just so that my players can have a shared experience with another group.
There is no reason that the players shouldn't know that the Emerald Claw are the soldiers of the Blood of Vol.
Unless that isn't true in someone else's version of Eberron. Unless the GM hasn't read that and doesn't know, so he decides something different.
Any player worth their salt can keep that knowledge out of character. If you want a plot element to surprise the player's, then choose something else, instead of one of the few "public secrets" of the campaign world (i.e. the secrets that anyone who reads the sources knows).
Well, that's all well and good, but any GM worth his salt can customize the setting in any way that he feels will improve the game for his players. If the players are enjoying themselves then it's all good.