While that's true on a faction level, it's obviously much easier to group people together based on what demi-god or god they follow. Yes you can argue that there are fringe situations where alliances happen (in 40k, you could use Desperate Allies or Come the Apocalypse to represent this), but on the whole in the fluff, the Fyreslayers and Sylvaneth both ally themselves with Sigmar. While the Stormcast and the undead have teamed up (in some pretty decent books, at that), it was a tenuous alliance at best. The Stormcast are loyal to Sigmar (duh) while the undead will never (can never?) go against Nagash's will.
I could accept there being allowances for certain armies or alliances, but honestly as I said above, the simplicity of Sigmar is one of the big driving points, and I think it would be more of a detriment to have an Allies matrix or 0 restrictions than it would be a boon. The simple Grand Alliance organization is easy to understand while still retaining mostly fluff sentiments, which seems as good as you could ask for.