I don't see much of a difference between the polymer SP-01 Phantom, and P-09.
There isn't much difference in size or weight, but the P-09 is available in .40 S&W (with a 15-round mag), and it has the Omega trigger system, which means it's convertible from safety to decocker. This seems to be a gun aimed at the LEO market as well as the private citizen market.
The SP-01 Phantom is 9mm only.
That's not to say that they COULD NOT have built a .40 version of the Phantom...
I suspect the P-09 is less expensive to build, and represents (along with the P-07) a new branch on the CZ tree.
I haven't seen or held a P-07, yet -- and it'll probably be a while before I see a P-09 in the real world.