For those who don't recognize the comparison, Battle-Cat is a really big green tiger that serves as He-Man's pet and steed. When He-Man is in his human identity of Adam, the cat is called Cringer and is a meek, cowardly animal. When Adam turns into He-Man Cringer turns into Battle-Cat, and is brave and fierce.
So, back to Krypto. In an earlier issue of Superman we saw a new, classic retriever version of Krypto which the Eradicator seemed to have created, or he changed the current direwolf Krypto. My idea has been since I read the issue that what Eradicator did was ingest Krypto, infuse the dog with Jon's genome (as Jor-El created Krypto initially with Kal's DNA), as probably a planned gift to Jon after it cleansed Jon himself. Thus the changed appearance.
Well, why can't Krypto be both at the same time? Say he now has Kal and Jon's genome within him. When he's docile and casual, he favor's Jon's genome and is the retriever. When its battle conditions, he favors Kal-El's genome and changes into the direwolf.