Because at the end of the day, they can say all they want that this is the real Jor-El, but all it'll take is another writer or editor to wipe it all away. They'll say it's an alternate reality Jor, mental manipulation on Superman's part, or whatever other excuse they want to go back to the status quo.
Remember Return to Krypton, where supposedly the MOS Byrne Krypton never existed and it was always a Krypton that resembled the Silver Age that he came from? I recall quite strongly that Jeph Loeb, Eddie Bergenza and others arguing that this was the Real Krypton, there was no way they were faking and trust them 100%.
We all know how that turned out.
So I'll be surprised if this remains the 'truth' in 5 years, let alone 20.
To be fair, they have a built-in excuse for Jor-El to have redemption because of the whole Clockwork Orange thing. He's not in his right head already.
I'm just worried they'll be using this to inject unnecessary drama for the perfectly stable Lois and Clark, making Lois resentful of her husband's heritage and Jor-El for nearly corrupting her son and damning her world, possibly making her like her father, and there will be maritial problems heading into Doomsday Clock. If this negativity is what I have to look forward to all next year (they've said every comic in 2018 is a prequel to Doomsday Clock) I won't be picking anything up until Doomsday Clock is concluded, and it had best end with the Super Family still in one piece.