You have to remember the planet was destroyed, so the history we get is best piece meal type. We know some space travel happened and at one point they even placed criminals in low orbit to serve sentences, then space travel was banned, and the Jor-el is working on it again. So somethings had to change from point A to point B to point C. but since all recors were lost it can only be pieced together as information turned up. all history is like that, not every bit survives thru the ages, example we know C Clombus discovered the new world (altho the people living there didn't know they were lost) but we don't know who made his hat, Minor point but an example. So it just makes sense to accpet something changed and the record of those changes is lost to explosion.
This does not work either as an explination either because Superman had visited Krypton's past
personally either as a phantom or phyically where he could try (and fail) to change history. Yet each time he did so the events he
peronally saw did not match the last one he had seen. Also if this was not bad enough Superman had other
methods to actaully see historical events as they
really happened rather as history said they happened.