Without the release of the rulings, it's difficult to say for certain, but I think it works out fine.
The commander is basically the same as
Parallel Lives, and one of the rulings for
Parallel Lives states:
"If the effect creating the tokens instructs you to do something with those tokens at a later time, like exiling them at the end of combat, you’ll do that for all the tokens."Seems quite reasonable to assume that this commander will work in the same way.
The design space for Fractals appears to be that you create a 0/0 and put +1/+1 counters on it based on some criteria. The same would be true here. You'd create twice as many Fractals, then put the appropriate amount of +1/+1 counters on all of them, so they wouldn't just die.
The key distinction here is that the commander is doubling the amount that you create, not creating copies of ones that already exist. If you were to create a copy, it would die as a 0/0, but that's not what is happening here. It's a subtle distinction, but it is there.