No, they can't make you install non-original equipment to pass emissions testing, but you need to be able to prove that is is, in fact, a "49 state" vehicle that has never been registered in CA, and you need to also be able to show what the original equipment was. If it was modified at any point, all the original equipment, no matter CA or 49 state, needs to be in place and operational.
Once, long ago, I brought in an out of state car with 49 state emissions equipment and I had to be sure that the proper federal emissions compliant sticker was on the fan shroud. Mine was missing so before I tried to register it, I bought a used fan shroud with the proper sticker, showing that it was 49 state legit. Without that sticker, they would have made me conform to CA standards.
CA used to charge an "entrance fee" of around $300 for bringing in non CA vehicles, but that rule was changed.