Indeed, banning "Races of Eberron" because Warforged, Shifters, and Changelings don't exist in your campaign and you don't want to flesh out the impact they'd have on the world is a legit reason. Banning it because you think it's broken doesn't seem terribly reasonable, unless I'm forgetting something.
Thing is, they don't need to have an impact on the world beyond what a standard-issue PC would already have (though that impact may be different than with a member of a more 'normal' race). Warforged are merely intelligent golems, while shifters aren't much different than lycanthropes, and changelings are hardly more noticeable than doppelgangers.
And who's to say that these oddball races aren't around, but hiding, or rare, or that you're not the only one of your kind in existence, whether as a remnant of an otherwise extinct race, a visitor from another world, or the experiment of a mad archmage?
D&D is filled with weird races. Denying someone something like this because it's odd is like Daddy forbidding Junior from ordering chocolate ice cream on his cone because Daddy doesn't like it.
However, there could be other legit reasons, such as WANTING extra-weird races for, say, a Planescape game where everyone's character is a newly-spawned petitioner or something.