We say under generate-id():

An implementation is under no obligation to generate the same identifiers each time a document is transformed or queried.

This is a very informal way of saying that the uniqueness rule is scoped to a single execution scope. It casually implies that there is a concept of node identity ("a document") that transcends execution scope, which formally speaking is not the case (although XQuery Update might suggest otherwise). And it raises questions about situations where a transformation or query can involve multiple execution scopes, for example when fn:transform() is called, or when XSLT static expressions are used.

I propose the following slightly more formal statement. After

"In other cases, the function returns a string that uniquely identifies a given node."

add

"More formally, it is guaranteed that within a single *execution scope*, codepoint-equal(generate-id($N), generate-id($M)) is true if and only if ($M is $N) is true." 

and move the sentence

"An implementation is under no obligation to generate the same identifiers each time a document is transformed or queried."

to the (non-normative) notes, since its meaning depends on informal notions of identity.