Very intriguing and also a little worrying.
I can see the Superman 2 setting, and the LnC villains. Interesting.
I think it very odd that Clark didn't - and still hasn't? - visited his mother on his return.
The Director grimaced. “Are you absolutely sure you can keep Atlas under control?”
“Sir, we have multiple precautions in place. And yesterday’s test was a complete success.
I think this conversation is very suspicious. I suspect that Atlas is Superman. 'Yesterday's test' could be the rescue of the plane. I don't think he's spent the last few years looking for Krypton at all. I think he was captured by the government to be turned into their puppet weapon. His sudden disappearance, and sudden reappearance indicates, to me, something out of Clark's control.
The government wouldn't realize that there was a 'Clark' to find a cover story for as well as the Krypton cover story for Superman. They wouldn't know that Clark would have family and friends that he would at least say goodbye to before disappearing to search for Krypton.
Hopefully Lois will somehow get some time with Superman and be able to figure this out and save Clark.