AEAD is a big example of that, delivering integrity protection for symmetric encryption that too many engineers never even realised their application required. Moving from the Merkle–Damgård construction to Sponge construction for hashes is one way to deliver another unspecified requirement - preventing length extension attacks.
Way too often in cryptography when somebody is sure that they don't need a big complicated system with a bunch of features it turns out actually they just didn't understand their full requirements, and as those become clear all the baggage they were pleased to be rid of turns out to have been necessary all along.
For a popular enough protocol, if there is an underspecified thing then there will be two implementations that implement that thing differently, and if possible, incompatibly. And I am talking about correctly programmed and compliant implementations, never mind the buggy and/or deliberately non-compliant implementations (cf. Microsoft's "No standard or clause in a standard has a divine right of existence" stance). That's why the designer should not leave the implementers any rope whatsoever to strangle themselves, especially in cryptography.
5 bits of choice is a lot of rope to auto-asphyxiate oneself in cryptography.
> Malleability. We also see no relevance of “malleability” to the standard definition of signature security. For example, if we slightly modified the system then replacing S by −S and replacing A by −A (a slight variant of the “attack” of [75]) would convert one valid signature into another valid signature of the same message under a new public key; but it would still not accomplish the attacker’s goal, namely to forge a signature on a new message under a target public key. One such modification would be to omit A from the hashing; another such modification would be to have A encode only |A|, rather than A.
They key here is the second half of the paragraph: "it would still not accomplish the attacker’s goal, namely to forge a signature on a new message under a target public key".
Similarly how the design doesn't see a problem with malleability in the sense of converting one valid signature into another valid signature, It seems to me it was never a design goal of Ed25519 to begin with to strictly define the set of valid (and invalid) signatures.
This is why cryptography is difficult, because it's easy to use a primitive in a complex system and assume things about the primitives that possibly make them unsuited for the system developed.
[1] https://ed25519.cr.yp.to/ed25519-20110926.pdf