Native not having alliance is completely fine for me, considering the lore and balance of power. As many have pointed out, a proper balanced alliance is quite tricky to implement because there are too many factors. The balance of power in a sandbox should be stable on its own (without player intervention) and a slapped-together alliance system would break that fast.
However, I'm of the opinion that Taleworlds should give modders the framework to implement whatever kind of alliance they want. For example, if a mod wants Spain and Britain to be in an alliance by default, and are more inclined to be allied throughout the campaign, they should be able to fiddle with the necessary factors to achieve such relationship.
I think this is the right balance for Taleworlds and players. Not that much work on their part because they don't have to fine tune the factors themselves, but still allows mods to make in-depth diplomacy.