It seems I was wrong - see Emre Yolcu's comment below.
My understanding is that that has not been accomplished (although the Quanta article is pretty vague so I could be misunderstanding the situation).
The Quanta article describes the following process:
Whip up a rewriting system which always terminates iff Collatz is true. This has been successfully done - but note that the termination problem is a priori $\Pi^0_2$, just like Collatz.
Try to find a collection of matrices satisfying some complicated constraints relating to that rewriting system. This is the task which SAT solvers are relevant for. However, they have not yet found an appropriate collection of matrices.
(This is where I was wrong:) Even after finding such a collection, we're not done. All that this will accomplish is reduce Collatz to a particular problem about matrix multiplication (which the Quanta article doesn't state - moreover, it doesn't explain why that problem should be more tractable than the rewriting one or the original Collatz conjecture).
Re: that third bulletpoint, I think that there's a particular part of the article which is potentially confusing:
“You try to find matrices that satisfy these constraints,” said Emre Yolcu, a graduate student at Carnegie Mellon who is working with Heule on the problem. “If you can find them, you prove [they’re] terminating,” and by implication, you prove Collatz.
It would have been clearer to write "If you can find them, you then try to prove [they're] terminating, and if you can you prove Collatz." That is, finding a system of matrices satisfying the given constraints - which is indeed $\Sigma^0_1$ - is only the first step, and the remaining fact we need to prove is presumably still $\Pi^0_2$.
Actually it seems I got that exactly wrong!
That said, pending further elaboration from Emre we may only have a $\Sigma_1$ sentence which implies Collatz - I don't know if the nonexistence of an appropriate matrix family would imply that Collatz fails.