Ed25519 private keys

RFC 8032, section 5.1.5 defines the Ed25519 public key A as a function of the private seed, and section 5.1.6 puts that A into the challenge the signature is built on. sign() therefore always recomputes the key pair from d and never signs under a public key handed to it: a -2 (x) that contradicts d is refused with an InvalidArgumentException, because signing under two different x values for one seed discloses the private key.

RFC 9053, section 7.2 makes x RECOMMENDED, not REQUIRED, for a private key, "it can be recomputed from the required elements", so an OkpKey may carry crv and d alone. That is the safest way to build a signing key, since nothing can then hand it an x inconsistent with the seed:

use Cose\Algorithm\Signature\EdDSA\Ed25519;
use Cose\Key\OkpKey;

$key = OkpKey::create([
    OkpKey::TYPE => OkpKey::TYPE_OKP,
    OkpKey::DATA_CURVE => OkpKey::CURVE_ED25519,
    OkpKey::DATA_D => $seed, // 32 bytes, RFC 8032 section 5.1.5
]);

$signature = Ed25519::create()->sign($data, $key);
$publicKey = $key->x();          // recomputed from $seed
$publicCoseKey = $key->toPublic(); // carries the recomputed x, without d

x() recomputes the public key for the curves sodium covers, Ed25519 and X25519. Ed448 and X448 have no derivation primitive in PHP, so a key on those curves still has to carry its x.