Those who deployed Argon2 must have deployed the reference implementation, therefore the code became the de facto standard. Khovratovich confirmed in https://github.com/P-H-C/phc-winner-argon2/issues/183#issuec... that the code is the de facto standard and the spec will be edited to reflect this.
libsodium implemented the same behavior simply because it reused the Argon2 reference implementation.
libsodium implemented the same behavior simply because it reused the Argon2 reference implementation.