The Emperor had created better Astartes.
But then he needed to create greater numbers of them in order to begin unifying the Solar System.
When he took Luna, he got access to the genecults up there. They had tech that enabled him to mass produce Astartes, whereas up to that point, it was more of a "small batch" operation. Many of the great Heresy era Astartes were Terrans who were created by this small batch process. Loken and Ahriman, for instance, were both of Terran stock, and not only were they titans in their early years, they just kept getting more butch as time rolled by.
I am not saying Primaris = Terran small batch Astartes. But I am saying the Emperor tweaked the recipe after the conquest of Luna in order to shift to mass production to fuel the Great Crusade, and that may have meant subsequent iterations were inferior to the Terran recipe. That plus ten thousand years of degradation gets you the current Astartes.
So, while I do think Cawl enhanced the Emperor's design, I think it wasn't new technological advances in gengineering, but more a cobbling together and retrofitting of existing gene-tech from the various product lines the Emperor had produced, with some updated armor (which doesn't seem to perform much better than Mk IV-VIII) and weapons (which likely are just up-sized and usable due to the increased musculature of the Primaris allowing for that sort of weapon.
Simply put, I think Cawl spent ten thousand years merging product lines back to the main trunk, and seeing what features he could successfully integrate into a new branch. And he likely did so with Heresy era geneseed from the vaults.
He didn't so much improve on the Emperor's designs so much as spin-off a new composition of existing technologies. There's probably a little of the Custodes and Thunder Warrior product lines in there, along with the Astartes and Primarch lines.
And Cawl had ten thousand years to do it, possibly with a significant portion of Martian gengineering capacity dedicated to the effort in secret. Possibly with the Emperor's own notes or direct experience from some of these projects, since Cawl is old enough to have been part of some of those processes. The Primarchs and Astartes took the Emperor a few years at most to start the line, a few decades to produce in bulk. And the Thunder Warriors pretty much came out of nowhere. Cawl has had millennia.
Cawl isn't a MacGuffin. He's a hacker and reverse engineer. I doubt there's very little in a Primaris marine that you can't find in another one of the Emperor's genetic tamperings.