The right strategy you need to fight the Progenitor is: NEVER let them get the Fleet Admiral rank!
Once the Progenitor gets the Fleet Admiral rank, their capital ships will start using the Light Granule attack, then you are almost certainly doomed! The best hope you can have in beating the Progenitor is to finish them as early as possible! For example, if you are fighting against 3 Expert CPU players and 1 of them is Progenitor, always kill the Progenitor player first! If you can't do that, you are certainly lost because the Progenitor only gets stronger as they level up, and by defeating all your attacking ships, they can level up fast.
But don't worry, I'm also a noob who don't always win even in his own mod! Progenitor is the strongest race given the Fleet Admiral rank, and I designed it that way; but I also designed a weakness for the Progenitor in the early game, and you can just use blitz tactics to beat one Progenitor player at a time. If you are fighting against 5 Expert Progenitor players using races other than Progenitor itself, then what I want to say is: please upload a video for that, it's going to be epic any way (EPIC FAIL, EPIC WIN, OR EPIC CHEATS) LOL~