Yes you can. I didn't say anything about you can't. But why is that a problem? You can win by a lot of things why shouldn't you win by a Fatal Blow if you have it? I said if you lose it's not only because of it. That means you have already lost a round and you were below 40% in Round 3 and you got hit. You could win by an X-Ray in MKX and was the two-hit instant armor more fair because you had 3 meters to perform it?
Then we could question a lot of tools based on the opponent has it but you haven't. You can have FB with 20% life and you're up gainst a Scorpion with a life lead. You must attack because time ticking down. Step, block, step, block, step, block, he's jumping back and forth, you have to attack or anti-air, boom, teleport, meter burn, you're done! Or you're up against a Baraka, he can delete your bar on hit with the Gut KB if you don't have full defensive bar to air escape from 40%+health so you can't even think about using your FB to survive.
You think being low on health is no cost, I think otherwise. It is a get out of jail kard in a way but you still have to make a read/time it properly/find a way to land it.
The only thing I'd change is the regen. If you whiff you shouldn't have it once again in the same round. That would make sense. But it is called Fatal Blow for a reason. You should be able to win rounds/matches with it.