There are many reasons why contracts are usually contracted — made compact, that is — by having them contained within one fully integrated document. The primary reason is that the “whole agreement” can be found in one place, leaving less ambiguity (one hopes!) about what the parties intended their deal to be. That way, it’s easier to enforce that deal, or so the story goes.
But just because that’s the general rule does not make that rule the best way to approach contracting in every instance.
In some cases, it makes more sense to accept more risk in terms of how a judge might see the “deal” in return for binding the other party to a set of terms that would never be possible, from a negotiating standpoint, if the entire arrangement were reflected in one document. In other cases, a multi-document agreement achieves what one document can never do: It becomes both stronger and more flexible.
In those instances, no matter how much more likely it would be that a single document would be enforced, it would not, by definition, contain the complete deal that you seek.
Breaking things up is sometimes the best way to make sure that they’re whole.